Unluckily, you only get it done like this at the present time, there is no general config that I know of.
If you have dozens of assembler files, then using inline assembly might be easier maybe?
However, the build process is under heavy development, and some day in the future, there will be a very much improved, generalized build system which will be a lot more configurable.
To get custom flags, you may try the "Build" tab instead of the "Advanced" tab in the source file's properties. There, you have even more options, but it is also a lot easier to break the build, of course.