No, no performance problems with a re-enable.
I might have found my problem. It seems restarting Atom is not enough to change the setting. I had to hit x on the console, restart Atom, and then issue the Open Console command.
I learned this because unchecking the fallback renderer option also didn’t cause any performance problem initially after a restart. The performance problems came back after I manually closed the console and reopened it.
It’s possible I manually closed the console after I unchecked the enable menu boxes.