Maybe, u can upload the picture of the side panel, both top and bottom and the size of the window that you want to cut.. Is it hollow between the plastic part and the metal ?

which area do you want to cut out ? I think cutting the metal part is not an issue but cutting the plastic is . ( or ask a laser cutter ) The plastic cover looks like curved or concave, so it is hollow and there is a gap between the panel and the plastic. If you attach the acrylic on the metal part, i believe you need to cover the gap, maybe use a rubber piece or maybe use the rubber floor carpet that they use for cars and modify a bit.

Yoda would have said : "A lot of planning to do, i see"

Just sharing some ideas, probably others might see another way