Thank you so much for your help, I've been stressing over this and smashing my head against everything for a while now :).
However, I didn't seem to catch how to fix the issue with the sail. I made sure the armature and geometry are at the same origin, but superpowers will only read the sail part, not the mast. Or is that the bug?
EDIT: I added two more bones to control the flag and superpowers couldn't read a mesh at all, and returned the error "No mesh found".
EDIT: Ok, after some heavy-ish analysis and comparison between other files that exported successfully, I accidently fixed the issue by duplicating the mesh inside the armature (?!) and creating a dummy bone whose vertex groups contains the entire mesh. That imported correctly, but the animation didn't. It appears to be moving on the wrong axis. Here's some gifs. I seem to be a bug magnet when it comes to superpowers :p
EDIT: Wait, my bad, I forgot to apply transformations to the armatures. I think all is well now :D. Thanks Elisée!