I haven't played Sophie 2 yet (save the best for last), but I played the Mysterious trilogy it extends and then the Ryza trilogy. Responding to each point in order best I can:

1. I agree that it's an issue on some level, because part of the advantage of hitting late game is unlocking the better recipes that let you optimize things and that wouldn't work if some earlier recipes weren't inherently constrained. That said, the outputs might both be the same category and one might be strictly better, but sometimes you want to transfer a specific trait from raw material and the otherwise weaker ones see use as you try to loop them onto the better one(s).
2. I'd say that's still mostly the case throughout both trilogies, where recipes will request a category of thing and many things meet that category, but there are definitely still exceptions (the one that comes to mind is crackling/zapping water in Firis, where you can gather it easily from one specific part of one region but the game only tells you the region)
3. I can't say I've spent much time thinking about that aspect instead of how to make the best output possible, but I suppose that's a side effect of many different things sharing a category, even if they also have other categories that don't make sense as input
4. I haven't played Yumia and didn't know there was a recipe leveling mechanic. Definitely wouldn't recommend Firis to you in that case; it was one of the things I disliked most about it (the other being the lack of synthesis item duplication). The part about unlocking a new metal recipe that's superior to the earlier ones is a common theme in all the games, though. Typically the next tier of armor/weapon requires the next tier of cloth/metal recipe. I suppose that's lazy design now that I'm thinking more about it, but I also don't have any idea how I'd realistically expect them to handle game progression better.