Electron Ionization and the Franck-Condon Diagram: vibrationally excited and vibrationally ground states
Why is it unusual (as it seems to be implicitly implied) that the bond lengths of the molecular ion in its ground state somehow end up being larger than the bond lengths of the molecular ion in its vibrationally excited state?
  


It's not so much about whether the bond length in $\ce{M^.+}$ is larger or smaller than that in $\ce{M}$; it's more about whether it's different. If you think pictorially about the vibration of a diatomic molecule or a spring, it makes sense that as you increase the energy (i.e. go to higher vibrational states), the amplitude of the vibration increases. The only way for a molecule to access bond lengths that are substantially different from its equilibrium bond length is therefore to be in a vibrational excited state.

Ionisation of $\ce{M}$ effectively always takes place from the vibrational ground state, so the initial bond length will always be very close to the equilibrium bond length of $\ce{M}$. If ionisation is almost instantaneous, such that the bond length cannot change during the ionisation, then $\ce{M^.+}$ is going to be generated with a bond length that is far away from its own equilibrium. This corresponds to an excited vibrational state. Whether it's larger or smaller than equilibrium doesn't matter; it just matters that it's different.

Of course, to say that this is the case presupposes that the equilibrium bond lengths of $\ce{M}$ and $\ce{M^.+}$ are substantially different. But this appears to be the assumption that the author makes. For more insight into this, @atbm's comments are spot on: the change in the equilibrium bond length will depend on the bonding character of the electron being removed. If a bonding electron is removed, then the bonds holding atoms together are weakened, and consequently $\ce{M^.+}$ will have a larger equilibrium bond length than $\ce{M}$; similar considerations hold for nonbonding and antibonding electrons.


  
  How does a situation arise where the bond lengths between such molecular ions differ so significantly that some end up in a vibrationally excited state and others in a vibrationally ground state? (If I had to give an educated guess, I would say that this is just due to random or non-primary factors.)
  


I suspect that the FC principle is no longer relevant to the adiabatic ionisation process. Adiabatic processes are associated with "slow" transitions: see e.g. https://en.wikipedia.org/wiki/Adiabatic_theorem, whereas the FC principle is to do with "instantaneous" processes where there is no possibility of the bond length changing during the ionisation.

This is not my area of expertise, but I will go out on a limb and say that the adiabatic ionisation process is largely hypothetical (at least in the present context). Wikipedia writes that 


  However, due to experimental limitations, the adiabatic ionization energy is often difficult to determine, whereas the vertical detachment energy is easily identifiable and measurable.


I am not sure what "error" the author is talking about, but my interpretation is that the adiabatic ionisation energy is the "true" or "actual" ionisation energy of the molecule; however, because physical ionisation does not take place in an adiabatic fashion, the measured ionisation energy differs from the "true" ionisation energy by ca. 0.1–0.7 eV.

So I would not interpret this as being two different physical processes that actually occur in the mass spectrometer; rather, it seems to be more of a thought experiment to me. Of course, I am open to being corrected on this.