All classes, except production where overboring is not allowed, have a maximum 1mm overbore limit. Read 8.1.1c. Though you do have a point Dave. He could overbore it 3mm as the class has no displacement limit but it would put the bike into Formula 40 heavy as it would now be about a 613cc motor.
you are confusing class displacement limits between open class and other classes. rule 8.1.1c. refers to class limit and not to OEM displacement of individual motorcycle. only open cc class has limit on OEM displacement for bikes that are legal for class as stock, all bikes 751-open that fall in this class can only overbore 1mm. however all bikes that fall in smaller than this class by OEM displacement are allowed boring and stroking up to class limit where they will race (same for formula.gp and sb bikes).
so, if your original bike displacement is lower than 751 your bike belongs to 601-750 class (there is twin and single allowance which I am not going in to now) and by boring it out 3mm it automatically becomes illegal for 601-750 class and legal for 751-open class. but since it was not 751-open bike to begin 1mm overbore rule does not apply to it.
in case of superdino this rule does not apply at all since displacement is unlimited and there are no classes by displacement, it is class for itself.
By your interpretation no bike there is bored more than 1mm or stroked would be legal in any class except FP. Lohmayer 450 or sv500 would not be legal to race in any class, those are just two as example.
this is because rule 3.1.1c is same for formula or sb or gp class and only excludes production classes where there is no overbore or stroking at all.