It appears that system_sam3xa.c is precompiled into libsam_sam3x8e_gcc_rel.a, which I discovered by attempting to copy the SystemInit functionality into variant.cpp, and getting the error that SystemCoreClock is already defined in libsam_sam3x8e_gcc_rel.a(system_sam3xa.o).
This appears to get compiled prior to the project compilation, as system_sam3xa does not come up in the verbose build output. Any advice on how to edit the version of system_sam3xa that gets compiled into this .a file, and where it would exist on a Windows machine?