This mildly frustrates me too, the reason you have to do this is because there is no option to add additional include directories ( As you have found ).
I have other needs when it comes to changing the command line call to gcc.
I have been thinking of writing a module for my server app that will intercept all the IDE's interaction with the file system, then modify the avr-gcc.exe call with my new parameters. If I continue the project I'll forward you the finished app.