I had this idea when looking at installing a mod downloaded from a GitHub repository.
I've come across a number of mods on the site that include documentation and screenshots in the Main file, which I will have to manually delete to keep my game folder tidy with only the mod files. This suggestions wouldn't really help as much with this problem, as it would be on the mod author to properly separate those out into the optional files, but I thought it would at least be nice for the option to include a file inside the archive that lists the non-essential files, so that the installer can ignore those, similar to how .gitignore works. If the source of the mod was GitHub instead of Nexus, then it may contain one of these files already.
I realise this is a niche feature, and implementing it wouldn't be a priority, but I just wanted to put it out there.