Hmm it kind of does. If you're in a cell with NPCs or creatures from a mod that would alter those NPCs or creatures, they won't be respawned fresh -- the cell you're in doesn't reset. If they're running code that's been updated (or in the case of FOOK, their inventory has changed) it could cause problems if data or references work differently or no longer exist.
Hence the safest thing to do to avoid problems is go into a cell with no creatures or NPCs (i.e, just static objects) and rest to reset cells.