I'm not sure any of the systems that are exclusively self tuning can handle nitrous or forced induction yet, but most that are manually programmable can. MSD makes a self tuning dang near all in one system that looks like a carb now (the Atomix or something I believe), that you pretty much just bolt in place of a carb, add O2 and coolant temp sensors, and a high pressure pump and off you go. MSD was asked if it could support forced induction and they said it was built with a MAP sensor that could handle boost, but the system couldn't just yet, possibly a software update or maybe some injector replacement down the road since a lot of people are asking.
However, you may be able to run a plate style nitrous system that delivers fuel and nitrous under a TBI setup (in my opinion at least). That way your nitrous system would be independent of the fuel system. Not sure how the cooler charge in the manifold might mess with the EFI though. The trick would be trying to keep the O2 readings the same with nitrous as without so the computer doesn't think anything is different when you hit the button. If you add extra fuel after the EFI you have to make sure you add exactly the right amount of air to burn it as well, that way the system wouldn't know any different (theoretically).
For example, on a mass air flow system, if you have a vacuum leak after the mass air sensor, the engine will run lean because it doesn't think that the extra air is there (didn't come through the sensor), so it doesn't add any extra fuel. But if you add an apporpriate amount of fuel to go with that air manually by some means, the engine will run correctly again, even though the EFI isn't the one correcting it. If you add nitrous to the system (oxygen effectively), you have to be the one to add the fuel as well, not the EFI system, similar to if you just had a carb (it doesn't really care what happens under it).