Specifically, I want to know what the commands are... all the flags it produces and passes to mxmlc. There must be a way, but I just can't figure it out.
Ultimate method - locate mxmlc executable for your platform, then create program with the same name which will log arguments.
If you just want to master mxmlc, there are docs for it and compiler option dump-config: -dump-config=config.xml. Config contains almost everything about the project and I used such config to make an automated build.