Read the full context of that rule. The entire section allows those provisions to be applied, it does not make those provisions. The APGLv3 disallows any further restrictions beyond the license to be applied, except for a handful of exceptions. That's one of them. And if such an exception is made, further instructions are provided to inform downstream users of them. Signal did not follow those instructions and didn't make any of the permitted exceptions.
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They own it, sure, but they license it out freely. They've released their work under a license that allows anyone use of their trademark, as long as they stick by the AGPLv3. The AGPLv3 is written permission.
I think what Signal is objecting to is that the snap looked like it was packaged and distributed by Signal when the files included could have been modified with a backdoor or whatever.