Thank you for your appreciation, I've just had a look at the numbering issue you mention but really can't seem to see the problem, the numbering in the files is in [y,x] format for each exported sub-map.
On my system (Win 10) even if I export ie. several hundred sub-maps they all appear in correct order in the directory (without any leading zero).
It would be easy enough to add (the next update will make use of an ini file for minor settings tweaks) but I'm just not seeing it.