Actually, the cockpit for the unused viper is identical to that of the Mark II, and in the closing scene of "Crossroads," Kara's Mark II is all CG, even in the close-ups where they would've normally greenscreened in the prop (and, in fact, did greenscreen the prop in the following scenes in "He That Believeth In Me"). My guess is that they considered having Starbuck return in a Viper from Earth instead of the one she died in, but either weren't sure or were unable to build a new prop in secret (or in the time left), so they intentionally designed it so they could use a Mark II cockpit in its place. The design, of course, would've been a (not at all) subtle clue about the twist that the original Colonists on Earth were Cylons, and that they were explicitly connected with the modern cylons. We probably would've ultimately learned that Viper was an ancient Earth design, and not contemporary as the characters would've assumed. But, in the end, they went in a different direction.
Apparently, even thought the Thirteenth Tribe Viper fell through, the idea of using a Viper design to show a common history between Cylons and Man has survived in the atmospheric Viper, which, with it's forward-swept wings, pentagon decal, and dual engines, almost looks more like a Raider than a Viper precursor.
