Having two sets of almost every upgrade is not great.
while they do have different crafting recipes they are not meaningfully different.

combining the ones that can be combined (into the core or possible a separate package) would remove unnecessary complexity

The two sets being separate is intentional and I don't have plans to merge them. Some of them are way more expensive (backpack stack upgrades) and them being separate gives modpack makers option to make one or the other set have different cost based on what the modpack is about.