It’s surprisingly no one has mentioned DaisyDisk or Grand Perspective so late into this thread.
When you get the warning, I recommend using Daisy Disk ($5-10) or Grand Perspective (free) to find out where the space is going.
It’s most likely has to do with iCloud archive and the setting of keeping files on disk.
Edit: aaaaand I just saw your post about iCloud issues. rofl. Strong suspicion it’s icloud backups taking up spacew.