The central charge $M$ corresponds to the translation operator for a fifth coordinate. The Galilei group has a five-dimensional representation that is best seen by considering the effect of an infinitesimal boost $𝛖$ on the kinetic energy $H$, momentum $𝐏$ and mass $M$:
$$ΔH = -𝛖·𝐏, \hspace 1em Δ𝐏 = -𝛖M, \hspace 1em ΔM = 0.$$
Together, it transforms as a 5-vector $(H,𝐏,M)$. For the coordinates $(𝐫,t)$, however, we have only the transform
$$Δ𝐫 = -𝛖t, \hspace 1em Δt = 0,$$
(with a similar transform for the coordinate differentials $(d𝐫,dt)$), and are unable to form an invariant 1-form with the coordinate differentials and mass-energy-momentum vector. What we get is:
$$Δ(𝐏·d𝐫 - H dt) = (-𝛖M)·d𝐫 + 𝐏·(-𝛖dt) - (-𝛖·𝐏)dt - H(0) = -M𝛖·d𝐫.$$
Thus suggests adding in an extra coordinate $u$ (and its differential $du$) with the transform law
$$Δu = 𝛖·𝐫, \hspace 1em Δ(du) = 𝛖·d𝐫$$
which would allow us to complete the invariant
$$Δ(𝐏·d𝐫 - H dt + M du) = 0.$$
This can be seen from the standpoint of Relativity in the following way. First, we have the proper time, denoted here as $s$ and a quadratic invariant which expresses it in terms of the differentials of the coordinate invariants:
$$ds^2 = dt^2 - \frac{1}{c^2} |d𝐫|^2.$$
Now consider the time dilation $s - t$. In the non-relativistic limit as $(1/c)^2 → 0$, it also approaches 0. However, when scaled up by $c^2$, the corresponding quantity $u = c^2 (s - t)$ does have a non-trivial non-relativistic limit! Upon substitution of $s$ by $u$, the quadratic invariant in Relativity becomes the following two invariants:
$$ds = dt + \frac{1}{c^2} du, \hspace 1em |d𝐫|^2 + 2 dt du + \frac{1}{c^2} du^2 = 0.$$
In the non-relativistic limit, this reduces to:
$$ds = dt, \hspace 1em |d𝐫|^2 + 2 dt du = 0.$$
The 4-dimensional geometry of non-relativistic theory embeds as a light cone in a 5-dimensional space whose extra coordinate $u$ bears the same relation to $M$ as $𝐫$ does to $𝐏$. This geometry is the Bargmann geometry and it goes with the central extension of the Galilei group which, itself, is called the Bargmann group.
In Relativity, instead of kinetic energy $H$ and mass $M$, one has the "total energy" $E$, which has the same transform law as $H$. However, the coordinates in relativity transform - under boost - differently:
$$Δ𝐫 = -𝛖t, \hspace 1em Δt = -\frac{1}{c^2} 𝛖·𝐫.$$
So, one can form an invariant one-form with them:
$$\begin{align}
Δ(𝐏·d𝐫 - E dt) &= (-𝛖M)·d𝐫 + 𝐏·(-𝛖t) - (-𝛖·𝐏) dt - E \left(-\frac{𝛖·d𝐫}{c^2} \right) \\
&= \left(\frac{E}{c^2} - M\right) 𝛖·d𝐫 \\
&= 0,
\end{align}$$
provided one equates $E = M c^2$, with $M$, this time, corresponding to what used to be called the "moving mass", which is no longer invariant, but transforms in Relativity as $ΔM = -𝛖·𝐏/c^2$.
You can connect this back to the non-relativistic case by treating the kinetic energy $H$ as $E$, itself with an invariant "rest value" $μ c^2$ of the energy subtracted out: $H = E - μ c^2$, replacing $E$ by $M$, and adding in the invariant $μ c^2 ds$ to write:
$$𝐏·d𝐫 - E dt + μ c^2 ds = 𝐏·d𝐫 - (H + μ c^2) dt + μ c^2 \left(dt + \frac{du}{c^2}\right) = 𝐏·d𝐫 - H dt + μ du.$$
In effect, that's the Relativistic version of the Bargmann geometry: a 5 dimensional representation of the Poincaré group with the invariants
$$μ = M - \frac{H}{c^2}, \hspace 1 em P^2 - 2 M H + \frac{H^2}{c^2},$$
which recovers Relativity, itself, as the special case where the linear invariant is set to a "rest mass" $μ = m$, and the quadratic invariant is set to 0:
$$0 = P^2 - 2 M H + \frac{H^2}{c^2} = P^2 - \frac{E^2}{c^2} + m^2 c^2.$$
More generally, it corresponds to the Poincaré group, trivially centrally extended with the inclusion of the central charge $μ$, which - in this generalization - may not be identified as any rest mass at all.
(Edit: I just looked at Weinberg. For notation, his "$H = M + W$" corresponds to what I'm writing as "$E = μ c^2 + H$". I always use $E$ to total energy - kinetic plus mass-energy - for Relativity, and $H$ for just the kinetic part, and non-relativistically for energy. He's using $H$ and $W$, respectively, for these in the discussion in section 2.4. So, for dimensional correctness, with my notation, his (2.4.22) would be
$$[K_i, P_j] = iħ \frac{E}{c^2} δ_{ij} = iħ \left(μ + \frac{H}{c^2}\right) δ_{ij} = iħ M δ_{ij},$$
and the same would apply in the non-relativistic case, except $M = μ$.)
As to your other question, in a Lie algebra, a central charge is any Lie vector that has zero Lie brackets with everyone else. Effectively, that serves just as well as a definition (it's not the actual definition, but it's a necessary condition), since you can always treat any linear invariant of a Lie algebra as the central charge of the central extension of a reduced Lie algebra; namely the Lie algebra obtained by setting the invariant to 0. For example, for the Bargmann group, the linear invariant is just $μ = M$, itself, and the Galilei group is obtained from it by setting $M = 0$, while the Bargmann group is recovered back as the central extension of the Galilei group with $μ$ as the central charge.
Now ... about boosts and translations; consider the effect of an infinitesimal translation by $𝛆$:
$$Δ'𝐫 = 𝛆, \hspace 1em Δ't = 0, \hspace 1em Δ'u = 0.$$
This time, we look at the coordinates themselves $(𝐫, t, u)$, not the coordinate differentials $(d𝐫, dt, du)$, since coordinate differences and differentials are translation-invariant. Does the boost $Δ$ and translation $Δ'$ commute?
$$ΔΔ'𝐫 = Δ𝛆 = 𝟎, \hspace 1em ΔΔ't = Δ0 = 0, \hspace 1em ΔΔ'u = Δ0 = 0,$$
but
$$Δ'Δ𝐫 = Δ'(-𝛖t) = -𝛖Δ't = 𝟎, \hspace 1em Δ'Δt = Δ'0 = 0, \hspace 1em Δ'Δu = Δ'(-𝛖·𝐫) = -𝛖·Δ'𝐫 = -𝛖·𝛆.$$
Thus
$$[Δ,Δ']𝐫 = 𝟎, \hspace 1em [Δ,Δ']t = 0, \hspace 1em [Δ,Δ']u = 𝛖·𝛆.$$
The result is a translation on the $u$ coordinate - i.e. the effect of the central charge $μ = M$ - as I originally characterized it.
How does this show up in the non-relativistic Schrödinger equation? Just consider the free non-interacting case, here. The equation is mis-characterized a part quadratic and part linear in the differential operators, and written like this
$$-\frac{iħ}{2m}∇^2ψ = iħ\frac{∂}{∂t}ψ.$$
In actuality, it is an expression of the linear and quadratic invariants
$$μ = M = m, \hspace 1em P^2 - 2MH = 0,$$
with the central charge $μ$ now identified as the mass $m$, itself.
So, it should actually be written as:
$$\left(|-iħ∇|^2 - 2 m \left(iħ\frac{∂}{∂t}\right)\right) ψ = 0.$$
The invariant 1-form
$$𝐏·d𝐫 - H dt + μ du$$
is directly connected to the correspondences
$$𝐏 = -iħ∇, \hspace 1em H = iħ\frac{∂}{∂t}, \hspace 1em μ = -iħ\frac{∂}{∂u},$$
which informs us what the operator form of $μ$ should be. So, when this is back-substituted with the choice of value $μ = m$, the result are the equations
$$-iħ\frac{∂}{∂u}ψ = mψ, \hspace 1em \left(|-iħ∇|^2 + 2 \left(iħ\frac{∂}{∂t}\right)\left(iħ\frac{∂}{∂u}\right)\right) ψ = 0.$$
The solution, as a function of $u$ is
$$ψ(u) = ψ(0) e^{imu/ħ}.$$
There's the extra phase factor. The coordinate $u$ shows up, essentially, as that extra phase you were wondering about.
Likewise, in Relativity, if you identity $μ = m$ as the rest mass, then the quadratic invariant previously derived is the mass shell invariant:
$$P^2 - \frac{E^2}{c^2} + m^2 c^2 = 0.$$
If you apply the same operator correspondence, as before, the result will contain the solutions for the Klein-Gordon equation.
As for "super-selection rules": a quantity that commutes with everything else gives rise to a super-selection rule. Every state is an eigen-state of a quantity that commutes with everything else; so the state space is block-diagonal, with one block for each value of the quantity.
So, the quantum state space is actually a hybrid between purely quantum and classical. In the extreme case of classical physics, everything commutes with everything, so there's a superselection on everything, and the state space is totally diagonal. In the opposite extreme case of purely quantum systems, there are no universally-commuting quantities, and the state space has only one diagonal block.
Recall that - in the Heisenberg Picture - the time differential of anything in connected to its commutator. So, if a quantity commutes with everybody and is not explicitly time-dependent, then it has zero time derivative. Correspondingly, there are no state transitions in which it changes. That's actually one of the main obstacles, by the way, of trying to hybridize classical and quantum dynamics: there's no clear way to get a back-reaction to the classical quantities from the quantum dynamics part of a hybrid system.
Weinberg is effectively treating the linear invariant $μ$ as something commutes not just with the other generators of the Bargmann group, but with everything else. Another way of stating this, in light of the operator correspondence just described, is that observables all be independent of $u$: a gauge invariance with respect to $u$.