Ok I tried it, apparently it does want to re-flash, not sure why but they may be doing something special for the cool alignment and cam features?
I didn’t flash it, because I don’t really want to use it as a controller app anyways, but I can help you out a little bit.
If you want to go all out, you could download the entire GRBL software, and the arduino IDE and customize and re-compile to suit your needs.
The stock firmware is on a wiki page.
http://www.shapeoko.com/wiki/index.php/Grbl
Default settings are here:
http://docs.carbide3d.com/article/38-shapeoko-3-default-grbl-settings