WRT to the bundle format being different, I may disagree.

The mod_overrides folder is structured such that it represents the internal structure used by the Diesel asset pipeline database to find the assets.
I would guess, based on some function signatures, that the asset database scans this folder, and then loads in the assets in a certain path to replace assets matching that path that are already in the database.

This would be pretty format storage agnostic if that's what they were doing.

One of the issues I suspect to be causing a lot of the functionality deficit on Linux is that (and this is speculation) overkill are using divergent branches for the Windows and Linux builds. This means that there are two effectively separate codebases being used for the two different builds. This would not effect the addition of new content such as Weapons, Maps, etc... because all that data is stored in bundles along with scripts that install them in to the game. If you look in to historic issues, many users were encountering similar issues during Crimefest 2015, such as not receiving voice data and what have you. Additionally, while I'm unsure of the date of its introduction in to the game, but I imagine that if you were to look at the source for the main/options menu, you would find that the "Mods" menu option (for the asset mods folder) is simply not even implemented