3500HD was offered through 2002. yes, the HDs are taller, but it doesn't matter, as they never came with a box. (from the factory anyway.....hmm, do i want to custom build a 11-12 foot dually box? )
The 2500s and 3500s sit higher than a 1500 IIRC, so the 2500s and 3500s are the same. but, the cab to bed mating should be the same, as the body lines need to match. so i think that any topper would fit the whole line, IMO.