MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
M3 is there because there are still a decent number of 20x20 stacks using M3 and M2 stack fits in M3 holes without modification or special hardware.
Plenty of M3 options still out there in the 20x20 range:
Omnibus F3 nano uses M3 (my preferred).
CL Racing F4 - Mini
If you rotate the motor mount like that motor wires will stick out to the side and boring holes down the length of the arm will compromise it's strength a lot.