Did you consider extending the bay down instead of up?
It seems to me that you could thicken the fuselage by a meter or so and give it a X-33/Venture Star-esque profile without ruining the overall "Altea Aesthetic".
The problem with extending the bay downward is the wheelwells for the landing gear - I've got something like 20cm clearance until I hit, and that isn't enough to make the cargo fit.
Bumping up the fuselage is theoretically an idea, but at that point, I might as well be making an XR5.
I've been chatting at Doug, and an option may be to make a ship that's specifically designed for STS-style cargos. That would come after this one, of course, so it wouldn't be coming out anytime soon. But maybe Tuesday.
You're correct in saying that I could probably tweak the profile to make it taller, but at that point, it wouldn't look the way I want it to look. I've spent part of today twiddling with a model, and it just looks ugly as hell. It's not what I wanted for this vessel.
Ultimately, I'd rather forge ahead with this model as I've designed it (and for the role I designed it,) and then do something afterwards that specifically fills the role of "Futuristic STS Replacement." That way, you end up with something that's actually designed for the role instead of me trying to shoehorn STS cargos into something that really wasn't initially designed for it.