To be honest, I think a hole punch would be problematic, not so much in terms of alignment but punching out a sequence of circular holes, to approximate a rectangular aperture, might be challenging, besides not having any control over width (diameter) of the aperture. Maybe there is a machine tool for hand usage that has variable punched-hole diameters.
What I did find is that, when you get to the point of creating apertures, one erroneous cut could be quite unforgiving and you might end up ruining all of your work up to that point. The further your progression into the project, the more careful you have to be.