Do you have set in both exports the same coordinate system? How much are these exports differ?
You can try to export the side ortho as Image (in coordinate system):
TWF file created from side view, Image:
0.1438256053 - X pixel resolution
0.0000000000 - rotation
0.0000000000 - rotation
-0.1439776282 - Y pixel resolution
_-1350524.4813268578 - _X coordinate of upper right image corner
128.9205650291 - Y_ coordinate of upper right image corner_
There are some strange coordinates for X axe, but the important thing in this case is the height (Y axe). You can change the X coordinate to 0 and the heights of the floors will be OK.
Also, about your request. The cross sections are 3D output, ortho is 2D output, so this is why it fits nicely on your point cloud.