I noticed some oddness with Glide64 in Banjo Kazooie's intro cutscene as well.
And ndk-stack is kind of useless for the exit crash unfortunately. Just the cryptic pthread_exit+80 log. It doesn't crash on my S2.
Edit:
some weirdness. These combinations of libraries can be unloaded without crashing (granted mupen crashes when loading a game):
mupen64plus-ui-console & mupen64plus-core
SDL2 & ae-imports
mupen64plus-ui-console & SDL2
mupen64plus-core & ae-imports
Edit2:
We have a race condition going on or something.
If I usleep for 0.019531 seconds or greater between unloading (mupen64plus-ui-console & mupen64plus-core) and (SDL2 & ae-imports), it doesn't crash (yes I bisected the time quite a bit

, 0.015625 crashed).
Now the question is, what is racing? Are the dlopen/dlclose calls asynchronous?