If you have no directory of command line tools and have restarted, your receipts may be stuck like [others have reported][1]. 

The process of removing these BOM files is not not normal but still the next logical step for you despite your characterization of it as an “utterly terrible idea”

> So I booted into recovery mode, disable SIP, moved all files from that folder that had **com.apple.pkg.CLTools** in their name, and the update in the App Store went away. Then I booted into recovery again to enable SIP

If you had a second Mac, you could save the dance of disabling and enabling SIP by putting your Mac in target disk mode and using another macOS computer to attempt removal of the BOM files

You also could do an erase install and restore from a backup only your apps and user data onto a clean system that hasn’t gotten the receipts out of sync with the installed developer tools. 

  [1]: https://apple.stackexchange.com/a/328089/5472