naw, any descent app shouldn't care about what order the options are in. Also, if they are using the standard getopts function (or even command for shell scripts), you can put any number of no-arg options after a single dash. getopts doesn't support the long form options however (i.e., --option-name)... hmm, actually, that's on HP-UX, Linux stuff is always far superior.
This problem was clearly caused by a compatibility issue with an older version of rsync and a newer version of portage. Unfortunately, I don't feel like reporting it as a dependency bug -- researching it, reproducing it and then dealing with the pain in the ass "RTFM-ers" that often troll bug databases, closing bugs for stupid reasons and bitching if you re-open them. Sadly, there are times when it just doesn't feel worth the effort.
All I care about is, that if somebody else has that problem, Google can give them a solution.