FWIW, our experience is that most of the folks using Linux want opensource apps — there are quite a few of them, and you ought to be able to find an opensource toolchain which will do pretty much anything you might want.
My first project on the Shapeoko was a locking register caliper:
It was done with pretty much all opensource software:
- the exception was it was drawn in Macromedia Freehand — Cenon or Inkscape could have been used (or it could have been programmed in METAPOST which is something I need to revisit)
- the drawing was made into a character in a font using Fontforge (there’s an issue on GitHub related to that)
- the engraving was done using that font in F-Engrave
- the outlines and so forth were cut using MakerCAM
- G-Code files were sent using bCNC