A lot of places won't pass an exhaust on a defected car, as it can come back to haunt them. A vehicle really does need to be engineered if it has any modification which can change its emissions.
Having said that, you shouldn't have too many problems passing emissions as long as you have a working cat converter.
The advantage of having an engineers certificate, combined with legal modifications, is that when you get pulled over, you have absolutely nothing to worry about.