The EMU is basically set up as independent from the std ECU, other than the global injector compensation, in general I have never needed to tweak the EMU for idle (unless you count the lag settings which can be a bit of a pain) and the same goes for low load/RPM, in fact with the Supra on a single turbo you shouldn't need to touch the maps (other than timing) until you start to make boost, as the std ECU does a very good job of things.
I think your saying that if the std ECU was not reset when the EMU was installed and then rest would it make the std ECU not correctly relearn the idle/lambda feedback? the answerer would be no, as its would just be normal feedback as the injectors are already compensated for with the EMU so the std ECU thinks its got std injectors, that why you really shouldn't even try to use the EMU for closed loop adjustment, as the std ECU will just fight it all the way to keep its version of stoic,
The only scenario that I can think of is if the injector change setup is incorrect, and the std ECU is trying to bring things back to stoic, and hasn't got enough adjustment, so despite trimming the injectors to reduce fuel it cant get things back.
Hope I have explained what I mean and not further confused things. LOL!