Is this because the German transports are considered part of the attack (amphibious assault)?
Yes. Transports that unload for an amphibious assault do so in the Combat movement phase (ending their movement for that turn), and so they are considered part of the combat force.
Ozteas 1941 is well reviewed. If you’re comfortable with some players being at peace at the start, that is also worth a look. Starts like round 3 of 1940.
Although if you prefer the simplicity of everyone fighting right away, go to g42!