Hey @Christopher_Fox ,
Welcome to the community! Feel free to Introduce yourself 
to the community if you want to! 
All of these are valid questions.
This is definitely not expected. We haven’t seen this before. Can you share the Speckle Model URL with us? If you can share the source Revit model too, that would be great.
As you said, technically, it is possible to compare two models (aka branches). It is a more of a UI/UX limitation rn.
I will let our web wizards answer your technical questions.