No offence but that is quite wrong,
Changing boost and ecu's WILL change emissions from the car. If you can prove that they don't (get an engineers report with an emissions test and appropriate gear to change emissions so they're equal or less than manufacturers specifications) then regency will not pick on you for that at all. This usually involves getting a very conservative tune and fitment of 2 catalytic converters so it can get costly.
Ive gone through 4 times in the last year, have had guages, swaybars, nolathane adjustable suspension bushes, brake bits and pieces, a tightly shimmed diff etc etc all fitted to my car and have passed through with them on. Last time i went through I had 4 guys look over my car at the same time and still passed.
They check over cars and make sure they are up to road standard, has nothing to do with stock or not. First time I went through my car was a dead stock automatic granny special and i had to replace bushes, tie rods, one suspension linkage and a few hoses.