Hi @josiahfce,
I admit that I don’t fully understand the issue here from your post but here is my answer based on my best guess.
When Pollination exports the model as TRACEXML it does several simplifications. You can see the full list here. The first item is that all the pitched roofs are translated to horizontal roofs. That is mainly because of the TRACE 3D Plus gbXML importer limitation. This is how your model looks like. The default approach is to keep the extruded volume as close as possible to the original volume.
If you want to keep the geometry the same trying using the gbXML file format instead of TRACEXML.
P.S. I have heard some news and the permission to share it from reliable sources that TRACE 700 is making a comeback! That will justify us rewriting the gbXML exporter to get all the useful information from Revit/Model Editor to TRACE 700. That should save you even more time in the process.