any reason not to cut it?

As long as you can get it to seal up. No reason it shouldn't work. But.... I'm a little leery on how ridged the pieces will be once cut. Flat tin doesn't have much rigidity without the bead or fold over work in tack. That's why it's designed the way it is.

He's basically going to make his air cleaner a three piece design.

correct
thats why i want to cut it on that spot, it will have a little bit of a lip still, and because its only sticking out about 2 inches from the side i think it will do just fine (plus, it will have the filter to support it )