In a situation where add-ons are overlaid like this, it’s inevitable that conflicts will arise. I don’t believe the game should restrict players from modifying the base files. Doing so contradicts the essence of modding and limits the game’s customizable aspects. What some might label as a “problem” could actually be an anticipated or desired outcome.
As @davux3 suggested, a tool to detect conflicts in the Virtual File System (VFS) could be beneficial. This tool could identify conflicts with installed mods or a specified set of add-ons. It would then alert the user about any potential conflicts. Making this tool a necessary step in the support process could greatly lighten the support team’s workload.