I don't believe any Viper is truly ideal in the atmosphere. The intake-like sensor array at the front is really just aesthetics-the real life repercussions of that assembly would be horrendous levels of kinetic heating from high-speed flight in the atmosphere. Drag makes heat! (which eventually damages/destroys structures...) The open thrust-reverser housings are actually quite novel in concept as far as space flight goes (and they look cool), but would not do well for the drag levels, either. Eventually, a boundry layer would form and possibly reduce the affects of drag "at speed." However, even a boundry layer has forces act against it. Thus, the situation aft of the cockpit is not great either.
On the bright side, the Viper is so rakish that it possesses a minimalist shock cone profile: about 18 degrees. This is pretty much the same as the SR-71, which can pull off Mach 3.5 at extreme altitudes. Now, at THOSE speeds, tiny little wings are great. The only problem is that the design is a paradox: It has a general profile which suggests tremendous speeds while having a potentially lethal drag problem which would cause huge amounts of kinetic heating. The obvious realization is that the Viper is made of unobtanium or the other super-elements. This is possibly good for a space ship, as its skin is so tough that it can resist terrible amounts of space-born radiation with minimal consequences (kind of like a lead wall...).
As for low speed flight, this would have to be achieved via having a very light airframe while flying at an extreme angle of attack (thus allowing those tiny wings to do their job; at least the Mk II has atmospheric control surfaces- the original didn't). OR you rely on thrusters. You'll note that the ones on the bottom are bigger than the ones on the top. However, as this method is not seen in series (Or at least I've never seen it. Then again, I've not seen BSG in full.), it might imply some sort of "anti-grav." Which would allow such unwieldy craft as Colonial One to fly in the atmosphere; it would also explain not having to "float" through the ship to get somewhere (though that's mostly due to the "filmed in the Hollywood basement" complex). It would also account for the "semi-newtonian" physics often seen in the show. That CERTAINLY would allow a Viper to make tighter turns in space if it's using gravometric thrusting as well as conventional engines/thrusters. Heck, Basestars use a gravometric drive to propel themselves through space, so it fits with the BSG universe (anti-grav on Vipers, that is).
@Enker: Mk I indeed refers to the TOS Viper. This may be incorrect notation, but I've seen it so many times that I consider it correct.