Is it possible to make different lines?
Yes. Each line would require a different building tree, however. You don't generally have them on a per-faction basis.
eg: A "roman" line, a "carthaginian" line, a "barbarian" line, a "greek" line etc already take up a tree each.
Now, with modfoldering, making sure the player's faction has its own line is probably the most important. It's fine if two barbarian AI factions can use one another's barracks line.
Now splitting stables and practice ranges across faction will be... yeah that's not a great idea, though you could have the unit recruitment require an appropriate level of barracks ... hm, though that would be confusing to the player actually.
For auxilia building probably a barracks or trader. For mercenary probably a trader and port.
That's perfectly doable. Multiple levels, or just one?
We won't have camillan units so no polybian reform. Just the Marian. However there needs to be other reforms for Carthage and the Greeks
I can't really help with script-based reforms, I think they work by changing some unconstructable building in every settlement.
I want to do the RS2 method with AOR. a1r1 a1r2 etc
Yeah, that's doable. Needs us to have finalized the map and regions before discussing which settlements fall in which "areas of recruitment"