I don't know why this has not been fixed. It's been the case for a while that the default /usr partition is too small if you intend to do kernel and userland compiles and keep up with errata in the stable ports tree. Maybe it's that there is an assumption that most users will not do this (they do discourage it, but it's the only way to apply errata). I try to remember to change the default layout on a new install; another option is to symlink /usr/src to a directory on a larger partition.