I think I can help out with this, and I have an idea. Editing the model I have to rotate the atmo wings 180 degrees shouldn't be too hard. I'll try to get that done soon.
In some of my Diaspora missions I used a model of an ejected pilot in his seat. I had written a Fred even in the mission where it's monitoring for a keyboard press representing "EJECT" in that case. And when pressed it would cause an explosion, black the screen for a second and change the player ship model to that of the ejected pilot. Without any ability to move at that point of course.
I could do something similar with two different Thunderbolt models, one with wings retracted and one extended.
If it can be done in FRED it should be scriptable too. So I was thinking of a script that does this:
Monitors for keypress "ALT A" or something unused. And checks if Thunderbolt change to Thunderbolt_Atmo, if Thunderbolt_Atmo change to Thunderbolt.
It wouldn't actually rotate the sections and you wouldn't be able to see that from outside, but it would allow you to toggle them after a fashion.