It seems like that sys-apps/systemd-tmpfiles-249.2 building process refers to the rootprefix variable, which is set in systemd-249.2 ebuild, but not in systemd-tmpfiles. So the building system decide the value as "/" or "/usr", which could cause the error "Prefix is not below root prefix...", when used in a prefix system where the system /bin is a symlink. Adding a line -Drootprefix="${EPREFIX:-/}" into the emesonargs seems to solve the problem for me, but I guess more work may be required to make it compatible for different situations(the systemd ebuild seems to do further process on the relevant parameter).
*** This bug has been marked as a duplicate of bug 806794 ***