I want to install a gas cooktop over a built-in gas oven in a under the counter cabinet.. I understand that this configuration is not normally done.. (installation is normally a gas cooktop with an electric built-in oven combination)...
Is there a code specification that I must follow for this installation, or this can't be done and why.

I don't think there is any code reason why you can't do this: both units should be designed so that anything can be installed near them. Check space limitations though - compare the depth of the cooktop plus the height of the oven plus the height of the kick to the total height of the lower cabinets.

Why not buy a combined gas cooktop/ oven? We got a 36" Wolf all-gas unit for our current kitchen and are extremely pleased with it. Link to Wolf 36" all-gas (http://www.wolfappliance.com/GasRanges/R36GasRange) There must be other manufacturers of similar products too.