Overriding files is the whole idea behind the VFS system. The issue you mention can be resolved by allowing JS files to be loaded in the DOM without having to override anything. This could easily be achieved on Asobo’s side.
A breakdown of what should and shouldn’t be overridable was already talked about here: [VFS] We need to find a way to stop this madness - #126 by SimbolFSReborn
This would create too much confusion for the user unfortunately. The solution should be dealt with at the source. Blocking all UI mods is not a solution.