I'm also confused by the diversity of ways to declare runtime paths. I found these linker flags related to rpath:

* -rpath=PATH
* -rpath-link=PATH
* -R FILENAME, --just-symbols=FILENAME: "Read symbol names and their addresses from FILENAME, (...). For compatibility with other ELF linkers, if the -R option is followed by a directory name, rather than a file name, it is treated as the -rpath option."
* --enable-new-dtags, --disable-new-dtags: "new dynamic tags in ELF"

configure and Makefile manipulates *compiler* flags, not *linker* flags, and so options like "-Wl,-rpath=PATH" is used: "-Wl,OPTION" pas OPTION as an option to the linker.