Biomes are a head-scratcher, but I feel like you could breeze through it with some laziness. Biomes like mountains, glaciers and deserts could just grow no plants, biomes like jungles, marshes, savanna could have the same plants that whatever the default biome of Stardew Valley is. There are actually some desert plants in Stardew Valley, I think coconuts and cactus fruit. Cold biomes like taiga could grow only fall crops and winter forage (like ice berry, winter yam), likewise warm biomes like jungles could grow only summer crops. You could also just have different names, taiga turnip, jungle melon, etc. (in real life tropical biomes, you only have wet season and dry season, not spring, summer, autumn winter, so a summer plant should be able to grow more often in a tropical biome, but I don't think DF would allow that.)
I wouldn't worry about the multi-harvest crops, DF isn't the same sort of time management game as SDV is, so there's no reason to try to emulate its time management gameplay mechanics. My intent is not to make a DF/SDV crossover, it's just to borrow SDV ideas to make DF more interesting. So likewise, with the forage/crop mechanics, just giving civs the OUTDOOR_FARMING and not OUTDOOR_GARDENS sounds sufficiently interesting to me. For dwarves, what I might do is keep them as only underground farmers to start with, and humans and elves get OUTDOOR_FARMING but not OUTDOOR_GARDENS, so crops and their seeds can be bought, but forage can only be grown locally. Disallowing their seeds could be interesting, to force players to use Gather zones.