In the eselect-java build system, src/scripts/run-java-tool.bash is supposed to be generated from src/scripts/run-java-tool.bash.in via (my EPREFIX=/disk/usr100/gentoo)
sed "s|\@GENTOO_PORTAGE_EPREFIX\@|/disk/usr100/gentoo|g" ./src/scripts/run-java-tool.bash.in >src/scripts/run-java-tool.bash
But the shipped run-java-tool.bash in the tarball hinders the correct process. It looks like a trivial mistake to fix by removing that file from the tarball.
I was already planning to make a change to eselect-java soon so I'll look into this soon.
Aha! jlec reported this today and I knew there was a bug for it somewhere but I forgot about this one. It's now fixed in -r1.