Well I figured out what is going on on my own here. A bit of a bug or weird design intent in Certificate Assistant when you have no CAs. It seems once you set something as the default CA you can't remove it from Certificate Assistant unless you have at least one other CA present. Looks like current behaviour is once you created a CA and set it as default, you from then on need a default CA so you have to have another CA to set as default. I did this to verify:
Assumes you have no other CAs at the start.
Create a CA Called "Test CA 1"
Then to remove it:
In Keychain Access Delate the certs for "Test CA 1"
Delete the $USER/Library/Application Support/Certificate Authority/Test CA 1/ folder
Notice in Certificate assistant "Test CA 1" is still present.
Create "Test CA 2" and make it default.
Close Certificate Assistant and reopen it and "Test CA 1" is now gone. Catch it now you can't get rid of "Test CA 2"