I started a new playthrough yesterday. And immediately, all the Guardian Perks were enabled.
I tested it by using Jump/Slam right after Claptrap gives you the Echo device.
Fair enough, they can be manually (one-by-one) disabled.
After getting to Sanctuary, I stopped off at Crazy Earls Shop in search of a Q-System, and was dismayed to find that all the weapons were anointed.
Also, the Black Market Vendor, their items are all anointed.
Anointments should be completely disabled until normal mode has been beaten.
They should be disabled if MM is not enabled.