I decided to use Boston Airport as my main base on my most recent play through. I had not used this spot before but since I was doing a BOS play through I figured it would be fitting. I found ways around most of the flaws that come with using this place as a normal settlement via mods.
The one thing I can't figure out how to fix, and its the most annoying thing ever, is Liberty Prime and his stomping around after you finish the main quest. I wish I could send him off some where or just shut him down before his stomping drives me nuts.
Looks like I will need to pack everything up, and boy do I have a lot of stuff, and move else where.