This makes installing Skyrim mods harder because mods often contain differing versions of folder names. For example one mod might be "Scripts" and the other might be "scripts". This means you can't have Skyrim mods on Linux if you're allergic to copying files manually as this will generally make mod managers not work as well. People on forums like nexus often have a hard time even grasping the concept of not using a mod manager so it's hard to get help of any kind.
I encountered similar with mods for Transport Fever which has had Linux native builds since the original Train Fever, but many mods have bugs related to inconsistent capitalization in the files that make up the mods. I haven't looked into if it works differently when running via wine/steamplay