Yeah this could be a problem. If they threaten to put tuners in jail, that could make things a lot more difficult. My car still has cats and all the emissions equipment installed, plus a catch can for extra measure
In July of 2018 the people here voted to end emission testing. It makes no sense to have to sit in line, pay money to have a car tested prior to renewing the license plate, when the car is brand new with a 10 year emission system warranty. Here it is 2021 (3 years later) and yep I had to sit in line yesterday to get the Hellcat to pass emissions to get the plate renewed. Seems three years later the paper work hasn't completed all the necessary steps.
They do not do a tail pipe test here on 1996 (I think that's right) and newer vehicles. On OBDII they just plug up and check for readiness of the emission monitors. I've been working on the car, and yep had to drive around to get the monitors to set, so I burned fuel so I could pass an emisisons test. Brilliant LOL.
As for E85, it does burn much cleaner than gasoline so if where you are does a tail pipe test it should be no problem, but if they do an OBDII test it will depend on how the tune is setup I believe. There are some tweaks to oxygen sensors and a couple other things to get it really working well that may impact some of the readiness monitors. I need to test that myself. I simply loaded my 93 tune to pass this year rather than fool with the flex tune passing.