I think comodo code signing certificate is one of the nice option to be added for Adobe Air, as i have seen comodo code signing certificate in other adobe programs. Recently i bought comodo code signing from https://cheapsslsecurity.com/comodo/codesigningcertificate.html, to sign one of my adobe application and it works fine, you can use microsoft authenticode technology with comodo code signing.
I do agree with concern that code signing digital certificate is the option to protect your Adobe Air Application, which would be contains .exe format.
Additionally, i would recommend that Code Signing Certificate market has been growing rapidly and I believe that the number of options has been there from other vendors. Let me clarify something on your need that if your budget is low then i would recommend your comodo code signing certificate, which is available in $67 from https://codesigncert.com/comodocodesigning or if your budget is high and bit lower that $67 then you should go higher trusted brands such as Symantec and Thawte as your aware that they are the most trusted Certificate Authorities in the world as per recent survey of W3Tech. If you want to know more about the Adobe Air Application protection through Symantec Code Signing Certificate and Thawte Code Signing Certificate, then visit official web pages.
You should go with adobe air 2 to generate native installers for application, It is required that you have EXE files for Windows, DMG files for Mac OS, and DEB or RPM for Linux to communicate with other processes using the Native Process. For further detail to sign your native installer applications click here.
To sing an Adobe AIR application, a software or application developer can get high assurance class-3 certificate from trusted certificate authority like Comodo, Thawte or Symantec. - https://www.ssl2buy.com/code-signing-certificate