So, I noticed while going around getting settlements on their feet that The Prydwen is listed as a settlement for some reason. That doesn't make much sense. It is a enclosed area that requires a load to enter. None of the other settlements are like that that I've visited. Is it because The Prydwen is part of the airport?

Yes. the Prydwen and airport are one settlement that has multiple icons.

Ahh ok. Thanks for clearing that up for me.