You can walk on deck as it is flying. I believe it is possible. A modder from oblivion called Reneer made a sailing mod. You could fully walk on ships as it sailed. The guy was a genius. This is a step up no doubt but im sure in theory its possible.
If you send vertibird to prydwen, it will stop and allow you to board then resume its journey.
This base would be like none other. Wear your power armour and jump down landing possibly anywhere you are flying over. Or get your settlement primed and ready as it along with it's vertibird escorts fly over your base if hostile with them.
I can see already many of you all thinking its ridiculously complex. Ask yourself this though. How did you think the people reacted when somebody first proposed a sailable ship in Elderscrolls Oblivion?
Nothing is impossible with a kick ass script extender and geniuses doing their scripts.