While the Steamworks FAQ states that Adobe AIR games cannot be wrapped, in reality that doesn't seem to be true. I test wrapped an Adobe AIR game and it worked perfectly fine. What I think they meant was games that use overlays may have problems finding the overlay depending on its search method. All overlay data is put into the .extra section and included as a part of the PE image in v2. If a game assumes the overlay starts at the end of the PE image or begins its search there, it will surely not find it. For programs that search the entire file, they should be OK as long as DRM components do not happen to match whatever is being searched for. For v3, overlay is completely truncated (for whatever reason), and any game that uses an overlay won't be able to run if wrapped with v3.
Note: "overlay" in this context is defined as the data that comes after a PE image but is in the same file as the PE image.