No, it won't take up a faction slot.
But the imperial reforms are/were being reconsidered by the EB team, since they take up unit slots and since it affects only the last 30 years of the game period.
Anyway, unless you cheat the first 200 years or so, you will be having a Roman republic, if the reforms follow the same logic as in EB I. Your two consuls will be the guys in charge for the year of their election.
IIRC there were rumours the teutonic tree will be used for the romans, which would be logical, because there was no "faction leader" or "heir" in ancient Rome. But only the EB-team know this for sure of course.