Hello, I just wanted to write that pkgconf 1.5 and later do support cross-toolchains. The procedure for this is described in pkgconf-personality(5) and should be easily adaptable for Debian's needs, as Fedora is using the personality support for the same purpose.
The upcoming pkgconf 1.6.1 release fixes some edge cases with this as well, so please consider removing wontfix tag :) William