Safari 13 update sets negative com.apple.quarantine -1 making multiple directories inaccessible

Ok, after wasting lots of time chasing this issue, I found one possible solution but it has raised more questions.

If I give Terminal Full Disk Access, the quarantine value shows the original values. Which means either the Safari 13 update also contains Gatekeeper system updates or Apple pushed an independent silent Gatekeeper data update around the same time.

More questions:

• Why was this working fine before? Terminal never had Full Disk Access permission.
• Note that Xcode still doesn't have permissions. That means I need to give Xcode Full Disk Access too.
• Why the huge difference in Time Machine backups post update?