Yeah, some products never went virtual. For "reference" there are reference cards and reference designs. Right now we are talking about reference cards. This happens only on mid to high end models. Low end models are pretty much always virtual.
While virtuals can be better, the flip side is that often the vernacular used in the industry is "cost-down." Translation: Make it as cheap as possible. Many companies do both. For instance the BFG 9800 GT OC2 and OCX cards were different PCB designs from the stock and OC cards, and were definitely built to a higher standard. All of them were virtuals because there were no reference 9800 GT cards that I'm aware of.
Cards like the GTX 280, GTX 295 (both versions) and the 65nm GTX 260 were all reference cards AFAIK. 55nm GTX 260, all GTX 275 and some GTX 285 were virtuals. The GTX 285 had two versions, P891 and P892, that were reference and virtual (may or may not be a hard line between them). Also, just because it is virtual doesn't mean you can't have Flextronics build them. The majority of BFG's virtual 260 and 275 were built by Flextronics (at a higher cost, but very slightly higher quality) and all of BFG's virtual 285 were built by Flextronics.