Hi @Tony!
I just wanted to follow up on this topic. I just finished a 2-month project (you helped me before here: Google Drive (G Suite) on macOS High Sierra) and I have some questions relating to these hidden files and count discrepancies.
I currently have uploaded ~11.56TB out of my ~11.57TB (on a Drobo, not that it matters). I have uploaded 847,441 items out of the 850,323 items counted on my Drobo. I was able to get these counts because I am using Google Drive’s File Stream, and they let you do item counts on the entire volumes as if they were local, really amazing stuff! 
So clearly there is a mis-match of ~2,882 items between the two folders. I found this topic after searching online, and when doing a test, I actually found 3,055 “Thumbs.db” files (I migrated from Windows to macOS a few years back), and 22 “desktop.ini”/“Desktop.ini” files. If I deleted those files, then I would actually have more files on the cloud than I would locally which doesn’t add up… Some folders seem to have more items after they synced to the cloud than they did before. Lots of little inconsistencies like this, which is understandable given the massive amount of data I have. I am curious, is there a way to turn off or edit the ignored files list? I’d rather have a few thousand useless/messy files on there than have mis-matched item counts. I’m just hoping to have more confidence that all, or nearly all of my files and folders have been synched. I have also looked into using the Kaleidoscope app, but I’m not sure how helpful it will be just yet…
It’s worth noting that before I started this process, I had over 4 million items. I spent a few weeks zipping up old folders with tons of files that I won’t likely ever need to access again. I will also do a few more passes on this since zipping up files is an effective way of masking these types of messy/ignored files. It also greatly speeds up the processing/syncing process after each restart.
It is unreasonable for me to shoot for nearly-exact-or-exact item counts for peace of mind? Should I just not worry about it? I’d love to hear your thoughts and hear any tips you may have to get closer to 100% accordance. I am also now more careful about adding ignored files and incomplete files/downloads with the leading “~” character from now on. Are there any tools that you’d recommend that are practical/safe?