1ZZ/2ZZ uses a fuel cut revlimiter. The Emanage needs to be wired into the stock ECU so it can send it the confirmation signals its expecting. Otherwise, it would store DTC's and light the CEL. It may even go into safe mode but Im not sure about that.
Probably throw a rash of P030X and PO13XX codes.
What sort of confirmation signals do you mean? Surely the ECU stops firing the injectors and just assumes the engine will stop accelerating? The car is pretty much guaranteed to be in open-loop if you're banging into the limiter without a downshift.
Yes, the ECU could tell that the car isn't slowing but it doesn't throw a CEL if you drop into 2nd at 66mph - the car just revs like mad!
From reading the EMU docs, it sounds like the EMU will just run the same injector pulses as it was running a couple of hundred revs below the factory cut-off. This is a bit crude, but should work, shouldn't it?