If I have to guess:
AquaMail must be using new versions of the FCM/GCM libraries (i.e. changed similarly to newbielink:https://github.com/vector-im/riot-android/commit/15bba9dce4a96e49fd4bd5132e2f60b57bdf1059 [nonactive]) These new versions are broken on my phone. This is because I'm not using Google's Play Services, but a reimplementation of them.
So, notifications (presumably) work fine except in my particular phone, because of the way I have it set up, and I don't expect anyone to fix it for me. I do appreciate Kostya fixing the crash, as now I have a test case I can use to potentially fix my version of Play Services.
Apologies if I sounded like I meant to imply otherwise. Thanks.