When /scripts/upcp runs, it executes /scripts/checkallowoverride, unfortunately there is no (official) way to disable it. However you can do:
Which will prevent it from happening. I'll see what can be done to make the application of checkallowoverride configurable. It's probably a legacy thing that someone requested long ago. It likely still serves a useful purpose for some, but should at least be configurable (meaning: run or don't run this script).
mv /scripts/checkallowoverride /scripts/.checkallowoverride
chattr +x /scripts/checkallowoverride