Is "Duae feminae habitant domi" also right?
Yes, that's acceptable, although the default preference in this case is for the verb to come last.
Except if you want to emphasize "home", as the place where they sleep.
Any emphasis is no longer the default, is it?
What's the diffrence between "habitat" and "habitant"?
habitat = he/she lives
habitant = they live
verb conjugation charts