I'm not an authority when it comes to answering this so I'll give what I think is right, until proper answers arrive:
1. In another mod I currently play, the number denotes if item requires 2 hands to use (green - allowed use but with acc penalty; red - other hand must be free to allow use). Not sure why or if Psi-Amp is a unique case here.
2. Don't know. I'm only worried about retaining OXC <-> OXCE
vanilla savegames compatibility, nothing else. Additional mods complicate things in unforeseen ways so you may not get satisfactory answer to this.
3. Only this
short list, afaik. I actually prefer OXCE way. If we were to load saves in OXC the game simply assumes vanilla behavior without loss of information (except additional UI options in OXCE).
LOS and other stuff, if indeed the case, may be unintentional case of undocumented changes. Those creep up over time and get increasingly more difficult to keep track of? Could be on your end though, since you mentioned mods. Residue in configs/rules/etc from pasts mods perhaps? Anyway, like I said, let's wait for proper authority as topic mildly interests me as well.