I think I fixed it! Thanks to the stock firmware dumps from TWRP installable stock firmware packages for Fairphone 3 I could run strings aboot.img | grep oem which gave me the following
oem unlock
oem unlock-go
oem lock
oem 8901_unlock
oem 8901_lock
oem device-info
oem enable-charger-screen
oem disable-charger-screen
oem off-mode-charge
oem select-display-panel
oem adb_enable
oem 8901_unlock certainly looks interesting, right? 
Indeed, running fastboot oem 8901_unlock now has the device reporting as in an unlocked state and boots up my OS again (I had to wipe userdata, but that’s part of locking/unlocking anyway)! 
For good measure I’ve also tried flashing vbmeta so far, which was succesfull, booting twrp and into recovery also works again.
So by the looks of it fastboot oem 8901_unlock can be used if you want to unlock the device without enabling unlocking in the android settings (or inputting the verification code). I haven’t verified this fully though.
I also don’t know if there are any differences between this unlock and regular unlock, so if you don’t have to, maybe you shouldn’t use this one. But as a last resort to unbrick your phone it’s perfect!
That said, I guess there’s no guarantee this will work for anyone else who have re-locked their phone without stock firmware, And I wonder what horrors you unleash by running oem 8901_lock. Given my experiences so far, I won’t try! 