Ill look into adding support for ignoring certain drives (perhaps something like the Spotlight ignore list?). Initially USBclean only displayed memory sticks, but I had requests to add to support more types...
I'm surprised that you're unfamiliar with such a long-established competing product. I provided a link to the BlueHarvest main page above, in lieu of copy-and-pasting a bunch of its explanatory content into this post. Perhaps you could take a moment to click that link and check it out? I would think that any differences would stand out to you immediately.
On Mojave, .Spotlight-V100 files can't be removed unless you give USBclean this extra access. Im not sure why these files are protected now, but the only way they can be removed is by giving USBclean this extra access.
If you don't need to remove them, USBclean will still function just fine.