mods don't have a "click territory on the map" button to get a territory ID
Yes, that is a definitely lacking. The Reconnaissance card (or Bomb card, etc - 1 territory popup) & Airlift popup [2 territories] dialogs really do need to be made available for use with mods (or just a N-territory, as many as required customizable by the mod), to let mods customize the text that pops up and act on the territories selected.
Compare the smoothness of bombing a territory even on a huge map vs the clunky usage of Nuking a territory where a custom dialog of randomly sorted (probably sorted by appearance on the map in some manner but random to players) territories pops up and players must (A) know the full name of the territory they're nuking, (B) find it in the nasty list, (C) be careful not to mix it up with similarly spelled [or identically spelled! Some maps have this] territories.