The issue comes down to ability to remove the top 1/3 or so of the frame and still have a frame with any rigidity.
I guess if you are talented at reinforcing the white metal commonly used on frames. You might be able to work with a SD40-2 (actual) model.
I just find it much simpler to use the more robust early split light board frame of the 40/45. Then fit HT-C trucks to that.
No matter how you do this. There is heavy frame alteration involved.
On my second attempt I actually laid the motor on it's side to get another couple mm off the top side to lower the car body.
This is NOT a shortcoming of the 3D shell, per se.
It reflects reality that a diesel hood is much taller at mid-point than an electric locomotive car body.
The only thing I do not think I would try using is a Kato mid SD40-2.
That chassis relies on the Kato plastic car body to hold it all together.
If you go with a classic frame 40/45, or an early SD40-2.
Stick with the version that has a screwed together split frame chassis.
Hope that helps.