Also, editing overmap_specials.json could be done by changing this section in each overmap entry (using the first entry, the crater, as an example):
"overmaps" :
[
{ "point":[0,0,0], "overmap": "crater"}
],
Including a tweaked version in a mod would allow you to mess with the map without bricking overmaps elsewhere.
Messing with regional_map_settings.json can be further used to affect what shops, if any, you want appearing in cities. Including an edited copy of that file in a mod SHOULD work.