It looks like what you are doing here is making the package do the work. Meaning that the configuration files are package dependent. Then your distroserver has to parse the files and then get down to business. What you are basically doing is asking developers to do it your way, and not their way. They don't like that. If they could agree to a certain way of doing things, they probably would have already.
I think there is a better way. It should be possible for the distroserver to run a ./configure just like any monkey, and then generate the configuration files by itself. Once a config file was created, it could be stored, to make installation of that package faster for the next guy.
I think this would maybe make the whole system more efficient. Because just about every program built with autoconf has --build-target=, --with-shared, --prefix=, and etc. The system can prepare canned answers to each of these, based on the machine, so you get a custom package. That leaves extra time and trouble for the optional components.
So, instead of going to the distroserver and asking for an FC3 package, the distro asks your computer what kind of package it wants. Then it builds a custom rpm (as an example) that is designed for your computer, on the fly, while you wait. This is time-consuming, but you can always use a little bandwidth to entertain during the process.
The reason to do it this way is that all you have to do are find the source tarballs. Every open developer has them. It wouldn't require anything more from anybody else than the current system (or lack thereof) already has. All the burden is placed on you and your program. Yeah, it will be harder for you. But it will be completely unobtrusive to everyone else. I mean, imagine what a pain in the ass it would be, if that sorta lazy programmer at ffmpeg didn't write an XML config file. You'd have to write one for him, and since he doesn't release anything but CVS snapshots, that would maybe be once a week. That's too much work, all because some lazy guy won't do things your way. It would be so much easier to just grab the CVS tarball, and have the machine do all the work.
All the users would have to do is download the app and/or visit the website - everything else is taken care of. It's like the way apt repos are done now, except there's no reason to keep extra binaries on hand for all the different possible flavors of Linux.
And best of all, if there is an important option for the package that I want, I get it. Example there is dvdauthor. It requires png15-devel, but only if the --enable-png flag is set at build time. Dag and Dries, in Fedora aptland, just didn't enable png, eliminating the devel dependency. But then you can't use pngs in your dvd menus. I had to download dvdauthor myself and configure it - the apt package was useless to me.
Just a few thoughts and experiences I have had that might help you design your system.