The problem is that a configure script takes a look at the system, right now, as configured by the end user, even with their home directory and whatever they've

The problem is that a configure script takes a look at the system, right now, as configured by the end user, even with their home directory and whatever they've shoved into env variables like LD_LIBRARY_PATH and then builds the software. At a minimum you need to have /etc, /usr/local/etc and ~/etc databases of "union mounted" layered configuration information, along with the ability to add and subtract arbitrary other locations where software might get installed. And it all needs to get updated with every new change to packages in those locations. As someone else pointed out in a comment, this is sort of the very unrealized promise of pkg-config. You can't do with just a static file/directory in /etc that defines the distro, that isn't even half the problem once you start installing stuff in /usr/local that you want to link against. This is a pretty good example of a Chesterton's Fence. You have to first fully understand why the fence is there before you knock it down.