The make file currently adds the prefixes to the pkg config files to
make it easier for tools that don't know about the prefixes used by dmd/ldc.

When i finally stop procrastinating, the plan is to split up GtkD and
start using meson and girtod to build the libraries, like what was
already done for GLib: https://github.com/gtkd-developers/GlibD

Can I suggest that asap is a good time to switch from Make to Meson?

In that case with the pkg config file generated by meson it no longer
has the prefixes.

Indeed.

I am willing and able to put effort where mouth is, and give a hand with evolving the GtkD build to use Meson if you are happy to manage me as a resource.