Not quite...
Every aircraft type has a TCDSN - a "Type Certificate Data Sheet for Noise". The specific noise an aircraft model makes in each phase of flight near an airport (takeoff, climb, approach, etc.) is measured and accredited by the FAA or EASA in conjunction with the manufacturer, and this information is published openly. It is the basis of the "noise certificate" that should accompany the other paperwork with your aircraft, but also databases of these figures do exist.
An airport can in theory find the TCDSN for each aircraft in its airspace, and can therefore work out how much noise it will make according to the ICAO Annex 16 requirements. They can then mathematically work out what the impact that aircraft has had in terms of noise over the area it is overflying assuming it is behaving as per the TCDSN measurements.
A "silent" aircraft will therefore have such great documented margins, the noise abatement procedures should take this into account, and no penalty should arise, in theory.
In essence it means the noise margins your aircraft has "on paper", in conjunction with following procedures can be rewarded/penalised equally even if somehow the engine is making significantly less/more noise than it should due to a problem. It can be - if done right - much fairer, especially if your engines are in need of a tune-up. :-)