Gotcha. Picture worth a thousand words and all that!
The IR detector is circled above in Red. It is a 3-terminal device with the optical sensitivity pointing "upwards" from the board.
The top of the case has a sort-of funnel that directs the received optical beam downward to the IR detector. This lens rotates on the top side which provides a bit of directionality - aim the flat sloped side away-from the handheld remote. On the inside of the rotatable lens the flat surface has a mirror-like surface which angles the beam downward.
The board attaches to the base plate with 2 solder joints so very easy to remove the circuit board.
So if I understand what you're doing, you have 2-wires in, 2-wires out. I suppose you could remove (de-solder) the barrel jack that accepts power. That way you don't have the bulk of the plug-in barrel plug. Or you could solder the wires to the jack solder pads on the bottom of the board.
If you are handy with a soldering iron, you can remove the 3-terminal IR detector and position it off the surface of the board by running 3-wires. This would allow you mess with directionality. You can buy IR detectors for about $1 if you're worried about messing it up. If you position the detector more than a few inches off the board you should add a resistor and a capacitor to act as a power-supply filter. Ask for more info if you go down this route.
Finally, just as with the rotatable lens/funnel, you can mess with your own lens to change the direction of sensitivity. Plastic or acrylic fiber, tubing, pipe, rod, whatever can make a low cost lens.