Two things:
Some Dish and DirecTV remotes can be set to RF so they don't need line-of-sight to receiver. Some BluRay can as well.
The HDMI matrix most likely includes IR repeating function. Mine did, the IR receiver and transmitter cables were in a bag in my drawer. They plug into the matrix and I mounted the receiver (a little block with cable) just outside the frame of the cabinet with wire going behind door. Then I plugged in two IR transmitters (little round red ends on cable) and placed in front of the receiver IR port and BluRay IR port. I also have an AppleTV in the cabinet but that works with Bluetooth to the remote.
While the repeater will only work by aiming at the receiver block it still allows you to close the cabinet. You just have to remember to aim the remote at the block. Won't work in the bedroom or outside unless you add another receiver block in those locations. More work than I was willing to do.
It also allows you to use the matrix remote outside the cabinet.
Maybe Brian can add this to the wiring in the rigs
Lastly: one can purchase a kit with IR receiver that transmits to a IR repeater that is placed in the cabinet. That could be moved outside when needed or in the bedroom. Again, I'm just happy with being able to have the cabinet closed.
I'm adding another thing here: Since my matrix had an additional HDMI output (#4) I put it to use for my bose wireless bluetooth headphones. Purchased a HDMI audio extractor and a Bluetooth transmitter and whenever I select a source for a TV I select that same source on output #4. That way I can turn down the volume on the TV and listen wirelessly (outside, inside, in bedroom) to not disturb wife or neighbors. Obviously doesn't work for local channels on TV (does not go through matrix) but I rarely watch those when I need to use headphones.