Is plexiglas transparent to the NIR (8-14um)? It might need to be thin to work. Some of the opaque plexi is better at transmitting NIR.
I have one of these same transmitters from dakota murs, although I don’t use it anymore as it sits out in the tree with dead batteries, but mine came with a wood birdhouse to hide it. That wood birdhouse had a single vertical wire and a single horizontal wire blocking the PIR window hole and I have not once had an issue. Either the wires work or your birds are more determined than mine. Just go with wire to start with, your unit is already waterproof and the manufacturer does that already.