Ideally, you want you'd want your HDMI run to the projector to be as short as possible to minimize any signal issues. However, a lot of times the projector ends up being mounted in the middle of the room, so it's about the same distance to the front as it is the back. From my experience, the ONLY advantage to having equipment in the front of the room is that you can just point the remote at everything and not have to worry about repeaters or IR/RF converters.
That being said, my current and past two theaters have had equipment mounted 1) slightly behind the seating, 2) just to the side and in front of the seating, and 3) in the back of the room. Neither of these options caused me any distractions or took away from the movie experience. My current build has the equipment in the very back of the room, which I do tend to prefer. It's also in a central point to the larger area of the basement so that is can easily be accessed during parties and get togethers as well.
Based on the PDF you just uploaded, I'd go with installing the equipment in the side wall under the stairs. You'd have access to the rear without any additional construction, and the heat would vent naturally through that cavity.