Yes, it does not matter which territory the troops on the transport are invading. The amphibious assault is in the sea zone adjacent to a territory with an airbase, which is all that is required.
Marsh
Let’s say a seazone adjacent to Southern Italy was being attacked and let’s say you had german planes in southern Italy. If an Italian ship was being attacked could you scramble a German plane?
yes
If you’re in a group game, proper etiquette suggests that you ask your teammate for permission, but yes… it’s allowed.
It’s not a matter of etiquette. The owner of the air unit makes the decision whether or not to scramble it, regardless of the controller of the territory it’s in or the owner of the attacked fleet.