I delete .dot_files littering FAT formatted thumb drives before using them on a smart TV etc via the Terminal with:
dot_clean -mnf [folder path]
But that does not touch those .Trashes and .Spotlight-V100 folders. I have not found a way to delete them via the Terminal ('ls: .: Operation not permitted' at least with sudo) but they do not bother me much so I have not tried very hard (.fseventsd can be readily removed).
I now again tested this and after revealing the FAT drive's invisible files via Shift-Command-. in the Finder I could delete .Spotlight-V100 folder but it soon re-appears unless Spotlight search for that volume is disabled via System > Siri & Spotlight > Spotlight Privacy... Oddly that does not reveal those .dot_files in Finder.