Creating local mod copy changes it packageId by adding "_copy", which cause loadFolders.xml of any mod to ignore that mod, when IfModActive being used. For example:

<li IfModActive="vanillaexpanded.vcef">1.4/Fishing</li> will ignore active local copy of that mod, since local copy now called vanillaexpanded.vcef_copy. VOE mod have additional outpost, if Fishing mod installed. But if local copy of Fishing mod being active instead, then VOE won't notice it and and you will miss additional outpost.

Which effectively cut compatability and additions for many local mods. Therefore local copies should almost never being active (unless you know that this exact mod won't suffer from this issue) and only being used as backups.
Doubt there is a good solution for that issue, so prob you can only make a notice for players about that.