GrapheneOS would definitely not support Motorola making some secret changes to the OS before installing it so this news is the complete opposite of such situation.

I completely agree, I am answering the hypothetical you brought up:

How would Motorola lock it down?

I don't believe they will lock it down, but you asked how could they do that. And the answer is they could easily do that, deals or not. I don't think they will, but there is nothing preventing them from doing so.