Hi Boilatas,
the side orthos can be tricky. Basically, there is no Z coordinate (it is replaced by Y) and only height can be measured there.
As you can see in TFW file created from side view, Image, you are getting these values:
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), which are basically Z coordinates and should be correct.
You can change the X coordinate to 0 and the heights of the floors will be OK.
Where are you trying to open the ortho? Also, the TFW file needs to be used for georeference the exported ortho, in other case it will be not scaled and in wrong height.