Download YAL sources, read the readme, it's explained there. Different qmake config options compile time. There is even script for that.
As for the home folder, yes, you're right. I wrote about that in gentoo bugzilla. Thing is, that this is not only about YAL, it's also about fs2_open where I have no influence where and how someone might patch his fs2_open to store config files/pilots.
As Chief said and as I described on gentoo bugzilla it's recommended to have a different binary for every TC. The above mentioned configurations for YAL change the path it looks for user config dir. But you _need_ corresponding fs2_open binary patched to use the same folder as well for it to work.