One reason is that all the other mods you wanted to use were redesigned to match the vanilla mechanics, so even if you use another mod to disable the vanilla mechanics, you're still suffering their consequences. They may even be redesigned in ways that require the vanilla mechanics.

You can't just remove the fields for a mob's armour items because all the mods that interact with mobs are checking what armour they have, and you'll get a runtime linking error. Best you can do is remove the code that spawns mobs with random armour so they always spawn without armour. There may still be armoured mobs spawned by mods.

In automation mods there was a concept called "sided inventory" where a machine block presents a different part of its inventory depending on which side of the block you access it from. When hoppers were added to the base game, they copied this exactly, but changed which sides accessed which part of which blocks to make them compatible with hoppers, because hoppers can only take items out of the bottom and put items into the top and sides. This affected all automation mods which, instead of using a more intuitive side mapping, use a mapping that makes sense for hoppers. Also, all other mods that add machine blocks now specify side mappings that make sense for hoppers.

Of course in principle you can rewrite the game and all your mods from scratch to match whatever vision you have, but I hope it's obvious that nobody would actually do that.

Even removing a single block or item is nontrivial. You can't remove the field because you'll get runtime linking errors from mods. You can't make it null. Even mods that don't rely on that item may be checking if a player is using it for some feature (and you'd like that check to always be false). There's a good chance many of the mods you want use it in recipes because it's available. Best you can do is remove the ways to obtain/create the item, and add a bunch of recipe overrides so it's not used in recipes either. If you have the mod that shows you a list of every item in the game, it'll still show up there.