I have to agree with F1ReB4LL on this.
When you are dumping/doing preservation work, you should not be hacking things to compliance or to "intended" values, even if that feels convenient and/or reduces number of dumps. You are supposed to be documenting the disc itself (not just the data that is on a disc). Nothing more, no less. If the disc is crap, you have to document a crap disc, not make it look nice and proper.
In my opinion, any other approaches would be exactly the same big NO-NO like an archaeologist discarding a fragment of bone or pottery because he has already thousands of very very similar fragments. Or to correct a grammatical error in an ancient script because what was actually written and what was intended to be written were not the same.
I agree that this approach may feel counter intuitive to the layman and that it is even pointless from a gamer's or rom collector's point of view. However, preservation is just coincidentally useful to these categories and should not be going out of its' way to cater for such needs. Documenting discs is the point here. At least that's how I understand the project.