I do have a working USB installer, but I can't compare the difference because I can't access the EFI partition on the affected SSD.
I've now 'solved' the issue by wiping the drive clean on a Windows machine, reformating it, and installing Catalina from the USB installer. I'm restoring my setup from a time machine backup (hooray for backups). Only 14 hours and 45 minutes to go. Then I have to restore the 'media' partition from my Backblaze backup which might take weeks.
Be careful with those Clover upgrades, everybody.