This $U(1)$ is just the gauge symmetry of electromagnetism. For a wave function of a charged particle, the $U(1)$ simply acts by changing the phase of the wave function. The "section" means that we actually want the phase at each point to be determined. But because there's the $U(1)$ symmetry, the phase is largely arbitrary. However, an arbitrary position-dependent change of the phase doesn't really create an equivalent physical state because the variations are remembered in the changes of the gauge field – in mathematical terminology, the information is stored in the "connection on the fiber bundle".
In the presence of magnetic monopoles, the vector potential $\vec A$ can't be globally defined because $\vec B={\rm curl}\,\vec A$ automatically obeys ${\rm div}\,\vec B=0$ but this equation is violated in the presence of magnetic monopole charges because ${\rm div}\,\vec B=q_m\delta^{(3)}(\vec x)$. However, it is still possible to define $\vec A$ almost everywhere around a point-like magnetic monopole except for a semi-infinite string (line) starting at the origin (the location of the monopole), the so-called Dirac string.
This is equivalent to replacing the monopole by a long magnetic dipole connecting the original monopole with the opposite pole that is sent to infinity. Because the opposite pole is at infinity, it becomes immaterial. However, the long solenoid (magnet) connecting the two poles must be invisible as well. A necessary condition for that is that the Aharonov-Bohm effect around this solenoid produces no detectable phase shift, and this is equivalent to the Dirac quantization rule for the magnetic charge, essentially $q_m q_e\in 2\pi{\mathbb Z}$.
In mathematical terminology, the possible transformation of the phase of the wave function induced by the trip around the Dirac string is why we need to talk about "bundles": it is impossible to set $\vec A$ equal to zero everywhere so even though there is no magnetic source anywhere in the space (except for the origin), we still can't assign a natural unique phase to the wave function in the bulk of the space.
In units of the elementary magnetic monopole charge, $q_m$ – the monopole number – may be expressed either as the coefficient of $\delta^{(3)}(\vec X)$ in ${\rm div}\,\vec B$, or – which is the same by Gauss' theorem – as the surface integral $\int d\vec S\cdot \vec B$ with the right convention-dependent coefficient. Also, because all the "nontriviality" of the bundle may be concentrated to the Dirac string, the only place where $\vec A$ isn't well-defined, the magnetic flux may be reduced to the integral over a small cross section cutting the Dirac string, and therefore $q_m$ is expressed from monodromies around the Dirac string which tells you how much the fiber bundle is twisted.
All these things are the same. To see why they're the same, it's useful to realize that physicists try to "trivialize" the fiber bundle and they almost succeed, except for the Dirac string where $\vec A$ isn't well-defined. However, $\vec B$ is defined everywhere except for the origin. So anything about the nontriviality of the bundle must be encoded in the gauge-invariant functionals of $\vec A$, namely in contour integrals $\oint d\vec \ell\cdot \vec A$ and surface integrals of $\vec B$. By the usual trivial Gauss-like theorems, they give the same number for the magnetic monopole configuration.
Concerning the updated shortlist of questions,
- the wave function is a section of a complex bundle with structure group $U(1)$ which is the gauge group
- the gauge transformations specify the transition functions between patches; the patches should be diffeomorphic to balls but in reality, we can make the main patch as large as the whole space minus the Dirac string
- the electromagnetic potential is always called the connection on the (gauge symmetry) bundle by the mathematicians; the inability to define $\vec A$ globally is why the bundle is non-trivial
- the value of the connection $\vec A$ can be anything that obeys Maxwell's equations. In 3+1D, magnetic monopoles are the only localized sources that can make the bundle nontrivial so every general potential is a superposition of the well-defined $\vec A$ and the $\vec A$ from a distribution of magnetic monopoles.
See also e.g.
can one introduce magnetic monopoles without Dirac strings?