Para - relative você precisa inserir um ponto no caminho do diretório de origem:
rsync -av --relative remote:/a1/a2/.../aN/./one/two ~/workdir/
Veja o manual:
-R, --relative
[...]
It is also possible to limit the amount of path information that is sent as implied directories for each path you specify. With a modern rsync on the sending side (beginning with 2.6.7), you can insert a dot and a slash into the source path, like this:
rsync -avR /foo/./bar/baz.c remote:/tmp/