Do you have an actual citation for this? Because as I remember there are cutouts, like if you make your own car.

A workaround may be selling it as a kit. If it's a kit and not intended for road use you could probably sell whatever you want, similar to selling radio kits that are illegal to assemble.

This doesn't mean it runs dirty, it just didn't pass inspection.

I'm not really a fan of skirting all EPA regulations, but passing them is a huge ordeal and probably not something a startup could do without lots of VC that would tell them to just emulate John Deere. It also covers exactly one engine setup.