As per discussion on the Arma Reforger Discord with @reyhard the initial GUID for a newly created .meta files seems to be based only on the path inside the current addon. So two addons creating the same path generate the same GUID right now.

To avoid this conflict the generation must be updated to maybe use the addon GUID (what is inside addon.gproj) as a seed. Or it precedes the current input path in the generation code e.g. GenerateGUID(addon.GetGUID() + "_" + file.GetPath())
That would mean that a GUID is unique per addon per file or at least the chance of a collision is drastically minimized.