On the "Alternative Factor" issues, we do see the crystals in a location that does not correspond to the other well-known location - the articulation frame under the floor of (one of the) Main Engineering control room(s). We see a blueshirt specialist handling them. We see Kirk's ship unaffected by the repeated thefts of crystals from the energizer, whereas removing a crystal from the articulation frame appears to deprive the ship of main power.
In "Mudd's Women", the ship came equipped with six crystals, after gods know how many had been lost to the Galactic Barrier in the pilot episode. Having four crystals at a time in recuperation would keep the ship operational - so Kirk would be pretty annoyed at the repeated thefts of recently reamplified ones, but not concerned about the survival of his ship yet.
My take on this still is that dilithium needs to be in an "energized" state in order to turn antimatter into warp power, and that "energizing" and "reamplifying" may be related to the "recrystallizing" that later allows drained crystals to be nurtured back to operation. However, the energies inserted into the crystal in this manner are not the ones released for applications. Rather, the energized crystal just channels other energies - antimatter aboard the starship, but inter-universe energies (which also have something to do with antimatter, according to the dialogue) in case of the technology of the two Lazari.
I don't know about that. I'd say the removal of the crystal from engineering isn't removing the power- it's removing the use of the available main power transfered from the nacelles. The crystals in each nacelle m/arc would no doubt be equally important, but remove the one from main engineering, and you're left with having to use the back up reactors that have significant less power because they're probably not m/am. There would be something with the way the systems are integrated that removing that main engineering crystal takes away the use of the warp engines despite their independent m/arcs.
But how and why would become the question. One point I make would be that it Starfleet ships being borded must be incredibly rare, and getting past security to get to engineering and remove that critical crystal would be highly highly unlikely, despite the Enterprise getting disabled so bloody often.
Now I say they would be a safer type of energy producing reactors because the main point of having the nacelles so far from the ship was partly due to the dangerous nature of the m/am reactors in them- and possibly due to the warp engines in whole themselves.