No more an issue than skinning a P51B with a malcolm hood on the old P51 (with folding canopy).
It's basically a non-issue, IMO. We can't have every minor variant ever made. What about spits with tall tails and short tails? Same plane, same engine, same armament, same performance, but one bit is different. We can't very well model every option ever had.
It's a compromise, and a fair one IMO. I do miss the old frames at times, but only for nostalgic reasons.
I would be interested in seeing if HTC can add the other canopy as an option. They can add a nose gun to the B-25, they should be able to add/swap the canopies, right?
Also, the Malcolm hood was fairly common. Maybe just not on the skins we have here. It was retrofitted after the fact, though, so you may see photos of planes with the framed canopy, that were later replaced with newer hoods.