If the files were in the wrong place, they wouldn't load at all.
You wouldn't see any side effects at all.
About the launcher not being "able to load them properly", it has nothing to do with any launcher what-so-ever.
This is an Unreal Engine 4 thing, controlled by bnsr.exe.
As long as the files are in the right place, they will be loaded.
But hey, some outfit mods can cause secondary effects, and sometimes they are unfixable.
Lets hope the modder will fix that issue.