You don't get the license without respecting the trademark.

e) Declining to grant rights under trademark law for use of some trade names, trademarks, or service marks; or

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.

Even without that, this is on their website.

Signal’s Rights. We own all copyrights, trademarks, domains, logos, trade dress, trade secrets, patents, and other intellectual property rights associated with our Services. You may not use our copyrights, trademarks, domains, logos, trade dress, patents, and other intellectual property rights unless you have our written permission. To report copyright, trademark, or other intellectual property infringement, please contact [email protected].

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.

Can you point me at the part of this document where 3rd parties are allowed to use your trademark?

https://github.com/signalapp/Signal-Desktop/blob/main/LICENS...

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.