I've got a Roper Whitney #218 punch press and do lots of square holes. You'd have to do some heavy modifying of a #5 Junior style punch to do square holes as neither the die or the punch are rotationally constrained. My #218 locks the punch and die from rotating so once aligned, they don't turn and scrub the sides.
Another square hole option is a nibbler. Couple of photos of ones I use are below. The top photo is of a popular one that runs around $12-$15. Think you need a slightly over 1/4" hole to fit the punch through, the nibble the corners. Lots quicker than filing. The lower photo is of an Adel nibbler which is a heavier duty punch.
Do a Google search for "sheet metal nibbler" and you see plenty of sources for the upper one. I bought my Adel off eBay (NOS) and replacement punches/return spring though I'm still on the original.
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