RUNTIME_PREFIX has such definition : 1. It is the directory into which uClibc runtime libraries will be installed (used during installation)! 2. Also shared library loader use it (compiled in). 3. Used for generation of $(PREFIX)$(DEVEL_PREFIX)lib/libc.so (Makefile.in:385). I think, it is hard to join definition of installation path and library loader path on developer machine (toolchain) in single macros. Or it is possible that there is bug - using of $(RUNTIME_PREFIX) with and without $(PREFIX) for same purposes (developer path). Look at Makefile.in:385, and so on.
i think the variable usage is just confusing you as documented in Rules.mak, PREFIX is like DESTDIR (base root where you install) as for RUNTIME_PREFIX and DEVEL_PREFIX, those are documented in the Kconfig help