OK, I now see the issue. Much more clearly...
The cross section is projected perpendicular to the alignments with the controlling alignment being the Horizontal NOT the vertical alignment...and yes this distorts the
tunnel section.
Good luck on any change to that coming from Autodesk.
Also I don't see any easy fix for this....However As stated earlier, on could resort to standard 3d solids EXTRUDE, or SWEEP command to model the tunnel and other features.
OR...and I have not tried this....Rotate the UCS and model this thing on it's side.....it may take a left and right version.