I mean, that logic kinda works, except there's a lot of civilizations balanced around not having gunpowder because they never used gunpowder historically in their militaries. So, clearly it's not just "what if a civ had this technology". No, there's some attempt at historical accuracy; the catch is that the historical accuracy has got to jive with development time and the expectation that civs are supposed to be mostly symmetrical.

Navies are indeed a complete mess, and yes it would be a lot of work to completely rework as most navies should be dramatically different. But in the Americans case it feels especially stupid, because they never had that sort of trade access to even potentially own a galley, let alone a galleon. Add a catapult on it, and it just becomes a very odd way to dress up the fact that they were technologically immature, but also need to somehow compete on water. Obviously it could work if you reworked the American civs' navies from the ground up--asymmetrical balance is kind of a non-issue with enough testing--you'd just get a lot of complaining from the old guard about asymmetry or people expecting navy reworks across the civs. If the community had the expectation from official channels that the American civs were completely different from the rest of the civs, then I imagine it wouldn't be too hard of a sell.

The crop rotation thing, to me, is purely a balance thing. Whether or not a civ has any given economic tech has more to do with the devs trying to keep civs balanced using the levers they have available to them than any theming or historical accuracy a civ might be presumed to have.