This is a map design issue, not a Bunker issue. Except that USF Base, that's just USF's unnecessarily complex base design. I don't know if the mapper can actually do anything about that...
Rotating the U.S. HQ object did not work for me on my maps. Rotating the HQ object of the other factions did work.
Easiest solution for Relic should be to place objects with sight/move blockers in the U.S. Base-bunker line of sight. Example Hedge_object or Tree_object.
Solo MG bunker objects can be moved easily backwards into the starting area.