I would not be afraid of running an Eagle 3.0L in the DeLorean and passing smog. As long as its tuned to pass the sniff test and the timing is stock, then you'd be okay. Most people doing the check will have no idea what to look for and the visual inspection just makes sure everything looks stock and no wires or tubing is hanging off. If you want to do a turbo setup you can just keep your old exhaust parts and put those on for the smog test. They're not going to rip open your car to find the Megasquirt ECU. There's a possibility you'll get someone who will give you a hard time but for the most part if everything looks and performs as expected, you pass. There are also places that guarantee passing but you won't find that advertised.

I got my stock DeLorean smogged this past year and the drone at the test-only center tried to fail me because of the atmosphere port tube on the fuel pressure regulator. He checked timing, emissions at idle and at certain rpm under load, and did the gas tank vapor test. I plan on putting in a turbo 3.0L with megasquirt and still being able to smog it.