As mentioned above, this is a common question. I would say don't drive yourself crazy over it and just forget it. Its clearly just an effect of Apple changing the algorithm that "defines whats what." My reasoning for coming to this determination is this. I recently performed a full erase and clean install of 10.13.4. I don't use time machine, and instead drag desktop, documents, downloads, and music onto my external Samsung T3. My photos are in iCloud photo library, and I like to cleanly reinstall all of my apps instead of migrate from a TM backup. After an erase and install, I drag back over the folders mentioned above, install cleanly all of my apps, and let photos resync from the cloud. After this process finished and I give my machine ample time to index, MacOS reports 399GB is used by system, and 186GB by downloads. Note that together this is 585GB. Now when I do get info on my desktop and downloads folders, it totals up to 594GB. Looking further into what is on my desktop, there is an almost 10GB folder of old photos in jpg format not imported into the photos app. Most of the files are mkv videos that takes up all of this space. The only thing I can deduce here is that MacOS doesn't like mkv as it is not a native container that Apple likes.
tl;dr: The system section of storage in about this mac is now useless.