Needless to say, this is really inconvenient. This is happening because the make recipe calls rustc with -o, which is ignored when codegen-units is present. Make will then always recompile rsbegin.o and rsend.o, since they aren't actually created.
The build still works for me, since the files aren't actually needed on Linux, but would probably fail on x86-windows-gnu according to rsbegin.rs (I haven't actually checked).
RUSTFLAGS should probably be ignored for these targets. I have no idea how, since the makefiles look like something straight out of /dev/random.