The way it should work is that during the OS install the OS can ask to have a cert added to the keystore at which point UEFI pops up a screen that says something like:

An application has requested to add a new certificate to secure boot which will allow new software to run at boot up. This usually happens when installing or updating an OS. If you would like to allow this press and hold <5 randomly selected letters> on the keyboard for 5 seconds. If you don't want to allow this press and hold escape for 3 seconds.

This would at least be a vendor agnostic way of enrolling certificates instead of the MS certificate just always being pre-installed. It should also of course be publicly documented exactly how the process works so everyone can use it.