When using #m2sync, compared to #mbsync, you need to use "maildirpp:" instead of maildir "maildir:".
Just though to mention since I was puzzling around this for few hours, and wondering why #notmuch finds everything, and aerc finds nothing.
EDIT: Had some issues with this but it seems interesting and relevant so I keep tracking this project. Now I at least got the mbsync bug fixed in Fedora.