It is not a problem technically, it is a problem from game play perspective.
I play at 28 day season, because that way, I do have a harvest (entire point of farming) before I reach the endgame. In other words, farming helps me reach the endgame - brings variety of food etc.
With 90 day season, the game pacing will be that I plant at mid game, and return to my farm in my deathmobil as a demigod, mutated and CBMed to the brim. Just to retire and watch my plants mature while sharpening my diamond katana on the grind stone.
In other words, with 90 day season, farming does not help you reach the endgame, it is something you do in retirement.
And if other progress like reading, crafting etc. is slowed down to match the real season length? The game will end up with pacing of grindy korean MMO, boring as f*ck.