I want to layout a power transistor based on the hybrid waffle design, which is a regular grid that looks like this. Except its going to be ~ 12x12 grid instead of 3x3. Does anyone had advice on how to generate this in magic? Ideally I would be able to parameterize the size. Should I do some scripting and directly manipulate the layout files instead or something?

I usually generate the .mag files with my generators. An alternative way is to use TCL, that way you can integrate it with a GUI into magic.

Do you have any example generators? It would be interesting to look through one

https://github.com/thesourcerer8/StdCellLib/ Tools/perl/