Something is definitely strange, this is most definitely not an integrated plugin and I definitely haven't set that flag in the code
I think reinstalling might be overkill, since you'll not lose any of your settings or installed plugins. But let's try the nuclear option
Start by opening Preferences again, then click
Miscellaneous, then click
Open calibre configuration directory. Go back and shut down calibre. Then go back to the folder window that opened, go into the
plugins folder, and delete anything that has "KePub" in the name. Restart calibre and try to install KePub Output again.