According to page 15 of the Pacific 1940 rulebook, the combat sequence uses this sequence:
1. Strategic and tactical bombing raids
2. Amphibious assaults
3. General combat
At first glance, this makes it look like you could use some sequence magic to get free transport kills, assuming your bombers got the airbase after suriving air-to-air combat. However, scrambling is the choice of the defender, and that choice gets made before you get to resolve any combat.
So, it’s not up to you – the defender can scramble before you attack the airbase.
Marsh