The solution for this would be to make the applications consistently load addons, by first looking in the first specified path, and only loading something from the second path if the addon was not found in the first one.
Right now, the only workaround for this very annoying issue is to not specify your PathToDownloadedModsFolder at all, and instead copy downloaded dependencies to your mods folder.
However, this workaround is extremely inefficient, since you have to manually re-copy things whenever any mod you are using as a dependency is updated, so I'm hoping for an actual fix.