Via Scott Granneman on the mailing list, ranman's answer on this question at Ask Different may shed some light on the accessibility permission low level systems.
I have no idea if those commands work, or whether they are safe or dangerous, but if they do work, then the versions for Keyboard Maestro and Keyboard Maestro Engine would be:
sudo sqlite3 /Library/Application\ Support/com.apple.TCC/Tcc.db 'delete from access where client like "%keyboardmaestro%"'
(that is one line, so be careful of wrapping).
Restart Keyboard Maestro and Keyboard Maestro Engine
Allow Keyboard Maestro access in accessibility via UI or something like:
sudo sqlite3 /Library/Application\ Support/com.apple.TCC/TCC.db "INSERT OR REPLACE INTO access values ('kTCCServiceAccessibility','com.stairways.keyboardmaestro.engine',0,1,0,NULL);"
sudo sqlite3 /Library/Application\ Support/com.apple.TCC/TCC.db "INSERT OR REPLACE INTO access values ('kTCCServiceAccessibility','com.stairways.keyboardmaestro.editor',0,1,0,NULL);"
(that is two lines, so be careful of wrapping).
Since, as far as I am aware, everyone has been able to get accessibility permissions eventually using the UI (it just takes some time and mucking around until the system gives in), I would suggest that is probably a better way to go that trying to mess around with low level databases like this which might well have other consequences.