[...] the meaning of the "$t$" which appears in spacetime intervals or metrics in general relativity. I concluded that $t$ was just a mathematical thing which allow to label the "spacetime manifold"
Foremost, coordinates merely provide distinct ("one-to-one") labeling of elements of a given set $\mathcal S$ by elements of $\mathbb R^n$ (i.e. by $n$-tuples of real numbers, for some suitable natural number $n$); and in particular of distinct events (i.e. of a particular "spacetime" set $\mathcal S$ under consideration). Formally, the assignment of coordinates is (merely) a map:
$c~:~ \mathcal S ~ \rightarrow ~ \mathbb R^n$.
Depending on further relations between elements of set $\mathcal S$ (geometric relations between events under consideration) there can be additional demands on coordinate assignments:
if elements (or subsets) of set $\mathcal S$ can be identified which are ordered (as a sequence) then a given coordinate assignment $c$ may or may not be monotonic, in one or in several coordinate tuple components, with respect to the "obvious order of real numbers";
if subsets of set $\mathcal S$ can be identified which constitute a topological space $T$ then a given coordinate assignment $c$ may or may not be compatible with $T$ in the sense of a homeomorphism with respect to the "obvious topology of real $n$-tuples". Thus the pair "$(~\mathcal S, T~)$" may or may not be a manifold; and if so, a given coordinate assignment $c$ may or may not be continuous.
if there is a (suitably generalized) metric $s$ available for set $\mathcal S$ then a given coordinate assignment $c$ may or may not be compatible in the sense of $s$ being differentiable or even affine, separately for any one coordinate tuple component (e.g. for "$t$", for "$r$", or for "$\phi$" etc.) with respect to the "obvious metric of real numbers".
In general relativity coordinates are assigned to events (generally) differentiable, or even smooth, wrt. the (given) spacetime intervals $s^2$; within any sufficiently "small" coordinate patch.
Moreover, the name "$t$" is not usually given to just any coordinate tuple component, but (only, if applicable) to one which is monotonous with respect to the sequence of elements of time-like curves, and monotonous with respect to the sequence of space-like hypersurfaces, and even affine with respect to the durations $\tau A_{\circ P}^{\circ Q} \equiv \sqrt{-s^2[~\varepsilon_{AP}, \varepsilon_{AQ}~]}$ of suitable participants $A$ (but, importantly, therefor not affine collectively to the durations of each and any participant).
1) $\frac{dt}{d\tau} = \gamma.$ If $t$ is non-physical [...]
Well, in the context in which this equation is derived, $t$ is not just any (arbitrary, one-to-one but otherwise "non-physical") coordinate assignment. With a more explicit and appropriate notation the equation appears as
$$\frac{\tau P_{\circ A}^{\circledS Q \circ A}}{\tau A_{\circ P}^{\circ Q}} = \frac{1}{\sqrt{1 - (\beta_{PQ}[~A~])^2}},$$
where
- $P$ and $Q$ denote two suitable participants at rest to each other
- "$P_{\circ A}$" denotes participant $P$'s indication of having been met and passed by participant $A$, and
- "$P^{\circledS Q \circ A}$" denotes participant $P$'s indication simultaneous to participant $Q$'s indication of having been met and passed by participant $A$.
2)
Consider an atomic transition at the surface of the earth, at [...]. The time interval
... say: the duration of any one oscillation period ...
measured by a stationary observer close to the atom is given by: $d\tau_1 = [...]$
... where it is of course completely irrelevant for the duration of any one oscillation period of the atom under consideration (at the surface of the earth) whether and how it might be labelled with coordinates.
Imagine now the same atomic transition but, say, 100 km above the surface of the earth at [...]. The time interval [oscillation period duration] measured by an observer near the atom is: $d\tau_2 = [...]$.
Since the physics of atomic transitions is the same [for these two separate atoms] then one should have: $d\tau_1 = d\tau_2$.
Rigth: that's what we mean by the oscillation period durations of these two atoms being equal;
or for short: these two atoms being equal
(in terms of the measure which is most relevant here, and or course regardless of any particular sprinkling of these atoms with coordinate labels).
But what is the physical meaning of the quantity $\frac{dx^0_1}{dx^0_1} = \frac{\sqrt{g_{00}(x_2)}}{\sqrt{g_{00}(x_1)}}$ ?
As far as
- the oscillation period durations of the two atoms are separately constant, and
- the coordinates are assigned such that both $g_{00}(x_1)$ and $g_{00}(x_2)$ are constants
then the "physical meaning" of the coordinates is that they are affine with respect to the durations of either atom, respectively.
But the additional, given or measurable fact that $d\tau_1 = d\tau_2$ does not further constrain the value of $\frac{\sqrt{g_{00}(x_2)}}{\sqrt{g_{00}(x_1)}}$.
In my opinion the only way to compute gravitational redshift is to compare the proper interval measured by an observer in $x_1$ and one in $x_2$ for an atomic transition happening in $x_1$.
In my opinion the most important and relevant chronometric comparison is between ping durations (cmp. my answer there: "An accelerating train ...", PSE/q/38377;
especially for observer pairs whose mutual ping duarions are (separately) constant, i.e. who are "chronometrically rigid to each other".
Only in reference to the unequal ping durations
of an observer "at the surface of the earth" (from having stated a signal indication, until having seen that the companion "100 km above the surface of the earth" had ssen this signal indication), and
of an observer "100 km above the surface of the earth" (from having stated a signal indication, until having seen that the companion "on the surface of the earth" had ssen this signal indication),
could they even conclusively determine that their separate atoms had equal oscillation period durations, in the trial(s) under consideration.
In particular: the number of oscillation periods which were counted "at the surface of the earth" in the course of one "ping period (100 km up, and back)"
is not equal to
the number of oscillation periods which were counted "100 km above the surface of the earth" in the course of one "ping period (all the way down, and back)".