Ambrosia don't just sell games that they make -- they also publish games written by other companies. DEFCON was created by Chris Delay and Gary Chambers of Introversion Software, and ported to the Mac with the help of Ambrosia. The version available in stores is the same game, but the not the Mac version. It is a Windows/Linux version. Your auth key from that version won't work with the Mac version, and your Mac auth key won't work with that version. However, players of the version sold by Ambrosia can play games against people using the other versions.
To attempt complete clarity, there are currently four ways that you can buy DEFCON:
Direct from IV (Windows / Linux version only)
Via Steam (the service run by Valve, the makers of Half-Life (Windows version only)
Retail (the boxes you see in stores) (Windows / Linux version only -- requires an additional download for Linux)
From Ambrosia (Mac version only)