Presumably a legitimate modification is one that is either factory approved/option or adaptation for a purpose... Van conversions/disability controls etc. As opposed to stretched tyres or egr deletes/piggyback ecus.
Noise and emissions are already on the V5, so easy enough to police on the MOT. Likewise the wheel and tyre fitments. Engine type/number versus the V5/registered details. A V8 conversion might be considered legitimate as long as the cats function and the engine number matches the V5... Current testing is based on the vehicle age, so modified vehicles over a certain age may have an easier time of it
The RPM Act is largely targeting independent aftermarket programmers/chip and ecu modifications rather than 'official' tuning companies such as Holley. Presumably companies such as Holley have the R and D budgets to ensure emission compliance.