When configured with just a --prefix=x and --target=y, $prefix/lib/../$target/sys-include used to be searched, for e.g. limits.h, stdio.h and stdlib.h. No $prefix-rooted path shows up as a "ignoring nonexistent directory" message either.
I don't know when this changed, but it doesn't seem like a deliberate change. Or at least, not an improvement. I'll open a PR if I can't resolve this. brgds, H-P