AFAICT, the CFG_MUSL_ROOT_X86_64 "variable" in the config.mk file that configure generates overrides the target.x86_64-unknown-linux-musl.musl-root setting in config.toml. I think the precedence should be the other way around.
cc @alexcrichton is CFG_MUSL_ROOT_X86_64 new-ish?