Is having a branch off the end of main heating HVAC duct bad and if so, why?
IMHO:

I don't believe the position makes any difference.  The pressure in the main duct, for all practical purposes, is uniform.  There is a slight loss at each exit duct along the main duct, but the original main duct should have been designed to handle this. However, if you added the duct to the end of an existing system, and the duct is comparatively too large-you can effect the air flow of the entire system.  Velocity changes with the duct size.