closed loop is the magic word here whatever ecu you are using.
the problem with std ecu would be its antitheft system and been upset by bits that may have been removed on your build (egr etc)
im not sure about omex (should do it) but i know it could be done with megasquirt2 or 3
you will need some form of closed loop set up. narrowband or wideband lambda in the exhaust.
this sees the exaust gas oxygen level and the ecu trim's the mix to suit
if your using programable this could simply be turned off after iva and on for mot
with a pc and cable (im thinking it would be best to have two maps one for power and one for mot/iva just push in the one you need but i can see your mot one getting used for one day a year
)
as long as your ign timming is good then i see no probs with fast idle and idle emmisons for mot or iva