I haven’t done anything with Asset Bundles, so I can’t comment on those.
The Resource folders being scattered aren’t too big of an issue. When Unity bundles the final product, it merges all those folders into it’s own tree. The bigger issue is what you put -=into=- the Resources folder. Since literally everything within a Resources folder is guaranteed to be packed into a game, and since everything that an asset in the Resources folder references is also guaranteed to be packed into a game, it becomes very important to make sure that all we add to the Resources folder are things we’ll actually want in the game…
In our game, we’re restricting the Resource folders to Inventory Items and Quests, so as a rule the bloat shouldn’t be huge.