Turns out the fix is very simple:
gsettings set org.gnome.mutter overlay-key ''
yay for simple solutions.
gsettings set org.gnome.mutter overlay-key ''
./john --stdout --mask=?1?1?1?1?1 -1=[a-z0-9] Press 'q' or Ctrl-C to abort, almost any other key for status aaaaa baaaa caaaa daaaa eaaaa faaaa gaaaa haaaa ...
./john --stdout --mask=?1?1?1?1?1?2 -1=[a-z0-9] -2=4 Press 'q' or Ctrl-C to abort, almost any other key for status aaaaa4 baaaa4 caaaa4 daaaa4 eaaaa4 faaaa4 gaaaa4 haaaa4 iaaaa4 jaaaa4