Why are the vias generated by magic not square?

Think of vias in magic like "VIARULE GENERATE" in LEF. It's an area of a contact, into which cuts will be placed, algorithmically, during GDS generation. The drawn via area includes the cuts and any mandatory surround that is common to both top and bottom layers. This works better with scalable-CMOS-type rules, where you can make the surround rules a bit conservative, enforce the same amount of surrounding material on both top and bottom, and so the contact just covers the intersection of two metal wires. It doesn't work so well trying to stick to the exact foundry rules, because mostly it just confuses people why magic's contacts are slightly larger than the foundry rules for cut layers. You can see the final cut layers in magic by doing, e.g.,

cif see VIA1

, which runs the GDS generation rules and displays the resulting GDS mask layer as a cross-hatch overlay on the layout.

I have no idea what half of what you said means. I just saw that for example the m1-m2 via is... directional? Like, they are two orthogonal rectangles. If I rotate them 90 degree it seems DRC still passes, but I can't make them any smaller.

The via layer in magic can be square. I probably need a screenshot to make sure I'm on the same page here. We might be talking about different things.

This is what magic generates for via1 of minimum size. Just wondering why met1 and met2 are sorta tangential rectangles