You only need to force the toolchain to build for an x86_64 target if you're not on an x86_64 host (ie. you're cross building). It's probably much simpler to just remove the -march flag from the compiler command than to keep adding more cross-building flags to other parts of the toolchain in order to get a native build.
I imagine the -march=i686 was added to the original Makefile to prevent builds for Pentium II or earlier CPUs which did not support certain faster instructions. The x86_64 architecture does not need to be restricted to processors available only in the last decades since all of them quallfy in that respect.