We are talking about ARM board, why AVRs are even here?
There are no significant vendor commands. The only vendor commands (at least publicly documented) are commands to get board information, which are not important at all for real development.
I don't know why the Open Source concept is so hard for some people to grasp. I guess it is down to decades of brainwashing that things must always be owned by someone, and now people can't conceive of any other system.
I liken Open Source to vegetarian food. If something is described as vegetarian, then it should contain no meat. It's really simple. In the same way, if an Open Source design has a programmable chip, the firmware must be open source.
What you are saying is "it only contains a little meat, you can hardly taste it, so can't we still call it vegetarian?". Obviously, no.
Mind you, I have met a few people who can't grasp the idea of vegetarian food either.
Note, we are not telling Arduino that their products must be Open Source, they are telling
us that their products are Open Source. It's entirely their choice. But it's misleading and stupid to put an Open Source label on something that is not Open Source, in the same way it is misleading and stupid to put "suitable for vegetarians" on a recipe that contains meat.