So I've been putting together a little process that'll make it easier. Flash itself isn't really intended to be used as part of a build process. It really wants to be a big polyglot build environment that has every possible build tool you'll ever need. Unfortunately it's never quite like that. Flex seems have changed that quite a lot with their command line builders and suchlike, but I'm too entrenched in Flash to bother with that.
And it's working. I now have games that'll talk to just about every high score system out there and a few custom builds for major game-portals. And if there's no high score system available, I now pop up an in-game leaderboard that works across all instances. Cool.
I'll probably update it on the play-n-share page today.