literally the only Animal Crossing that allowed multiple towns on one copy was Gamecube Crossing, due to it saving the town on the memory card with no limit on how many cards you could use for a single system
You can have more than one game per 3ds, - maybe that is what you have read - there are a fair number of players who have a cart copy and a digital copy on the same 3ds - or you could play two cart copies (Or more) on one 3ds.
Cart copies save to the cart, digital copies save to the SD card.
Personally I would find using one system for 2/2+ games difficult to manage - presumably changing the ingame time to play each game; you can't visit each other's towns, so couldn't share items, and only one game will be able to street pass. (the last one played?? Not sure about that).