Hi flow cats don't work any near as well as factory cats. First, the fact that they flow more means they have less surface area for the catalytic reaction to occur. Second, most aftermarket midpipes only have two cats located down under the floor. The OE midpipe on a 2003 had 4 cats, two right up by the manifolds and two under the floor, each doing a specific job.
If the MIL is on it means the cats are not dealing effectively with unburnt HCs. The exhaust content coming out of the cats is not far off what it is going in. That's what the rear O2 sensors are there for, to monitor catalyst efficiency, not total exhaust flow. The front O2 sensors are used for fuel feedback. Their signal swings between 0.2V and 1V (give or take) as the mixture is adjust lean and rich, respectively. In contrast, the sensors on the output side of the catalytic converter should be producing a much smoother output, varying little if the cats are doing their job because the chemistry of the exhaust gas is much more consistent. In fact, this is what MILs do: They are simply an electrical low-pass filter for the rear O2 sensors that smooth the output voltage fooling the PCM into thinking the cats are fine.
If the cats are inefficient in terms of the catalytic reactions, MILs might help get rid of the MIL but they won't help you pass an IM240 rolling-road test. It's one thing to fool the PCM with a LPF on the rear O2 sensors but you can't change the exhaust chemistry with a MIL eliminator. For that you need a decent cat.
AirCare claims to do "tampering inspections". They may be satisfied to see cats there though I don't know if they will know they aren't factory cats. If they don't do an OBD-II readiness check, you can erase the codes in the parking lot of the inspection station and try the test. If the exhaust quality is bad enough to make the rear O2s unhappy I doubt you'll pass though.
If you fail, you're going to need to source better cats or perhaps a stock midpipe: Bolt it on, test it, then put your high-flow setup on afterward. I went through this with my MRT catted-H and finally had enough and just left the stock midpipe on. Just went for DriveClean (Ontario's version of AirCare) and the car was cleaner than it was 7 years ago...