Maybe you should have provided this kind of informations in your original post, how anyone what supposed to know that ?
Then you should go ask on some IntelliJ support forums.
So far, the standard are the Flex SDK and AIR SDK command-line tools, they are documented and can be adapted to build on the command-line with many other tools: bash, make, ant, maven, etc.
If "IntelliJ relies on his own configurations" then it is a problem with IntelliJ toolchain, not the Flex/AIR toolchain.
Maybe you can compile on the command-line with IntelliJ tools, maybe not, look into the IntelliJ documentation.
That's fine, but you are overlooking one crucial thing: it's not your IDE that should dictate how to compile on the command-line but that's your original compilers tools.
I worked in teams where developers use many different IDE: from Flash Builder, to Flash Develop, to IntelliJ, to Visual Studio, to others ... and one thing I know is at the second you tell your dev you have to use this particular IDE then they are all stuck to use the same IDE.
But if you organise your build based on the command-line tools, everyone can share the same build process and use whatever IDE they want.
So the part "compile thru IntelliJ", I think it is a fail.
Keep using your IDE for local build if you want, but the build process should only be focused on command-line tools and ignore IntelliJ settings or special configurations.