I'm in the middle of a playthrough now, with 8 bases and getting close to 10 crafts. I just noticed that they are really all over the place.
Would it be possible to define a listOrder entry for crafts as well, which would be used to order them. Then if multiple crafts of the same kind are in a base, order them by ID. Somehow it works for vanilla crafts, you get:
Skyranger-1
Interceptor-1
Interceptor-2
when creating a game, but once you add modded crafts they go all over the place.
Having the same ordering in the interception screen would be handy too:
Skyranger-1
Skyranger-2
Interceptor-1
Interceptor-2
Firestorm-1
(etc.)
Grouping by bases is not really that convenient. The order within a base is still messed up and you can't reorder bases besides by editing a saved game.