No. You must clear the sea zone of all defending units before the amphibious units can land and attack. The only exception is if there are only subs and/or transports in the sea zone at the time that your ships enter it, in which case you can choose to ignore them and conduct the assault. However, if you choose to attack them, they also must be cleared in order for the assault to proceed.
Let’s suppose a DD and a loaded TR launch naval combat and amphibious assault against a defending DD & TR. If the two DDs knock each other out, leaving only the transports, does that mean the amphibious assault fails because the defending transport was not cleared? Seems a little rough if that’s the case
And would the attacking transport be forced to retreat or could it choose to remain in the same zone with the defending transport?
Very interesting point, but I think this is covered by the OOB-rules: On page 31 it is said: “… A transport cannot offload while in a hostile seazone. Remember that hostile sea zones contain enemy units, but that for purposes of determining the status of a seazone, submarines and transports are ignored.”
In your example the sea combat - as the first part of the Amphibious Assault sequence - ends when there are only transports left. So the land combat phase will start. For unloading from the attacking transport the status of the seazone at this moment (the very beginning of land combat) is still “hostile” but the “defending” transport can be ignored. Land combat can start.
That is what I read from the rules.
But let’s see what Krieghund says…