Overall, my feeling is that it would be a good idea to create the PC file as part of the build process but it's not going to be a substitute for "polyc". "polyc" was originally intended as a convenient way to compile and link programs written in ML for users who are more familiar with the compile-and-link model of languages like C than the read-eval-print loop of "poly". It can also be used for the linking step alone.
I would assume that there are autoconf macros available to automate some of the process of creating and installing PC files. If there are then that would be the way to go. There seem to be quite a few packages that already create PC files if the list on my Debian machine is anything to go by. I'll have a look at their autoconf scripts.
I'm not so keen on trying to reproduce the functionality of pkg-config with a poly-config script. It's probably better to encourage users who want to go down that route to install pkg-config directly.
There seem to be a number of applications around that are built around linking object files exported with PolyML.export. I want to try and find convenient and portable ways to do the linking process.
David