ChefJackButler,
Iben is most likely right about it being a matter of customer resources; I would guess it is that more than anything else, even dev time. I watch a lot of PZ builders on YouTube that do a lot of intricate construction, and they've said that when the piece count for builds gets too high, the game starts lagging, glitching, and/or crashing. Especially if the zoo also has a lot of animals and/or guests inside. I think I was watching a PaulsLey video once where he was like, "I can't actually open the zoo and let guests in, or the game will crash." I don't know the technical terms for it, but basically the user's computer, the software, or both can't keep track of all of the different variables at once. And given the number of PZ YouTubers who clearly have quality gaming setups, I think that says something about how resource intensive PZ can get. I imagine this is the real reason why--outside of sandbox mode--the habitat population limits are what they are, not just for the American Alligator, but also for the American Bison (which can and do live in much larger groups in the wild than they do in PZ) as well as others.
Frontier is actually really good at researching the animals they put into their games, and anywhere you see population downgrades like this (including brood/clutch/litter/etc sizes for offspring), it's often proportional to the real-life statistics; I highly doubt that this population cap has anything to do with their development team knowing nothing about gators (or the other animals whose populations have been limited in this way).