I believe that dockerMan already does support other registries on 6.9. (https://github.com/limetech/webgui/pull/650 unless I'm misreading what this is for )
Tomorrow, once the change actually takes effect, I will be testing whether it's a container pull or an image pull (multiple images in a container) that counts towards the quota. Realistically, it shouldn't affect many users around here (uber power users and some developers being the exceptions). On a quick look at the coding, it's not that hard to add in dockerHub credentials to the system to allow you 200+ pulls every 6 hours.
But, yeah if you're checking for updates to your containers every hour, then you may run into it.
CA itself doesn't particularly care which registry is used. There's a few apps currently which do not utilize dockerHub.