I you mean the paths stated inside .pc files, then pkg-config on
windows should be able to automatically deduce the correct value for
${prefix} based on the location where said package is installed [1]
and ignore whatever is stated as ${prefix} inside the .pc file.
No adjustments should be needed.
This was made so by tml way back, when he used to "./configure"
and "make install" each package into a separate prefix, stringing
things together (both for build and runtime usage) as needed
using PATH, PKG_CONFIG_PATH, ACLOCAL_FLAGS and other env vars.
Quite elegant, one can test (build and/or use) different versions
of packages fast, without having to go and build a complete
"bundled" distribution for each test (unless there's ABI breaks off course).