You literally cannot mess with your emissions system legally…

First of all, that's a Clean Air Act thing with limited purpose and scope, not a blanket restriction on owners' right to modify their property. Moreover, it is certainly not a restriction imposed and enforced by manufacturers that somehow justifies making the software closed-source and DRM'd. I want to make it clear here that, by supporting closed-source vehicle software, what you are really supporting is private enforcement of laws instead of government enforcement of laws, which is incredibly fucked up.

Second, it is not true that the act of messing with the emissions system is itself illegal. What's illegal is the act of using the vehicle on public roads afterwards. You can use your emissions-system-modified car off-road or on private property (e.g. farms or racetracks) all you want.

Third, the way that law is implemented is, frankly, bad and wrong anyway. Instead of saying that parts need to be EPA-certified (or, in practice, CARB-certified) to be legal to use and that the ECU has to report "ready," what it should do is say you can modify it however you want but that it has to pass a real "stick-a-probe-in-the-tailpipe-and-actually-fucking-measure" emissions test instead of a bullshit "visually inspect and plug a computer into the OBD2 port" test.

...nor can you disable or modify certain safety systems (seat belts, etc).

No, that's a lie. It is perfectly legal to swap your factory seat belts for a DOT-approved and properly-installed four-point racing harness, for instance.

I don’t need your massive multiple ton machine bluescreening down the highway or locking up the breaks randomly because you installed the wrong module.

That sort of thing could already happen for decades due to people fucking up their mechanical modification of the brakes, yet that's always been allowed. In practice, it isn't actually a widespread problem because people aren't actually as suicidally moronic as you seem to think they are, and that isn't going to magically change just because a computer is involved. Your argument is nothing but exactly the kind of fearmongering that I'm calling bullshit on.