Brian, if I am understanding your question properly, piping a hydraulic separator the way you have described would cause a pretty big problem. When you’re putting the boiler piping into one side of the separator with supply on bottom and return on top and the system into the other side with supply on top and return on bottom you will be forcing the boiler supply and system return to mix before going to the top boiler return or the top system supply. When this happens you will essentially be mixing down the temperature of the water going to your system and mixing up the temperature of the water returning to your boiler. This would lower the capacity of your heating system for sure, but as to how much, I can’t be certain.
I’m glad our literature is keeping everyone on their toes and questioning what may not be best practice!