I am not expert, but I think these will become collectible. Giant is a pioneer of bicycle carbon fiber, they are one of the few companies that wove their own and you can be sure that most bicycles (specialized and trek for example) that were made with carbon tubes in the 1990s were made by giant or their tubes were sourced from them. I am not saying that is a fact but it is a fact that giant is a large supplier of bikes and was a large carbon supplier to other companies.
The last layer of carbon, from my understanding is an aesthetic layer. I believe they did that on purpose to expose the carbon structure. Underneath that outer layer the resin would obscure the clean woven look of the fibers. So I would say there is no guarantee that your opaque painted Cadex will have the same top layer as the clear coated one. Is this a real difference? Probably not. and I might be completely wrong as it doesn't make a lot of sense to produce different tube finishings for aesthetic reasons.
I would guess that Giant was developing their carbon fiber technology on a yearly basis, remember Giant bought the tooling from Germany to make tubes when they thought it might be a good material for bikes. They were leading the industry. The raw spools of carbon were sourced from Japan. I would guess there is no difference for models in the same year, but I would say that it would not be unlikely for them to be changing up the weaving, diameters and thickness, and even resin composition on a yearly basis in order to improve the product.
__________________
1 Super Record bike, 1 Nuovo Record bike, 1 Pista, 1 Road, 1 Cyclocross/Allrounder, 1 MTB, 1 Touring, 1 Fixed gear