With regards to your "C" shaped model above. If you check the dimensions on the final ISO you'll find that indeed the piping is properly dimensioned. Viewing the dimensions reveals the top and bottom horizontals are indeed parallel at a 45 degree skew.

Isogen does not produce isos to scale. The top horizontal leg appears at that offset so that Isogen can fit the dimension lines without overlapping other pipe or information - that's just the way Isogen works with pipe skewed to the major axis.

I suspect the same issue with your image above, but I can't read the dimensions to verify.