when using the mods folder most files related to editing update.rpf reside in there so that's tidy enough, same with scripts in dll format placed the in scripts folder. It's just the asi scripts with their own folder (in some cases) that clutter the base game folder a bit

regarding viruses, all uploads are being checked by VirusTotal when uploaded, in the 5+ years I have never encountered any issues in this regard

I suggest you check out ikt's guide for getting started and in case of any other questions use this forum or our discord where most long time modders reside