Didn't see this, so apologize if this is already implemented.
I have some mod, that if loaded into //Mods do not work (mod name is ElectricityOverhaul) but when copied to /Mods works perfectly fine.
Would be sane to add option on Cloned game installs to install modlets into 'traditional' Mods folder.
This would be similar to what isolation for overhauls does.
(another note on this particular mod - it's auto install BepInEx so technically it's jumping out form sandboxing)