Hi paczek,
welcome back to the forums!
I understand your approach. Personally I like it more to have the ship selected after unloading units, because then I can reorder the ship to another place.
Therefore I'd suggest implementing a new option in the settings where players can decide whether they like the auto-selection of unloaded units or ongoing selection of the ship.
Another question is, which setting should be the default one. If an implementation into the main game becomes possible, the Gameplay Discussion forum would be the right place for a request for comments.
As far as I understand the development of 0 A.D., this would qualify for a pull request.
Best wishes, obelix