Hi,
I tested $subject again with 1.24, and it's improved significantly. Geany now installs geany.pc and the development headers properly, so the plugins build without problems. The plugin installation, however, creates a \lib directory on the installation drive, with all lib<pluginname>.dll.a files, which is completely pointless. It was the same with 1.23, but I forgot to mention it.
The prefix problem is workarounded. Since geany.pc is installed in \geany\path\lib\pkgconfig now, win32 pkg-config automatically uses /geany/path, replacing \ with / and ignoring the prefix setting. If you move geany.pc into \geany\path\lib, as in 1.23, the setting becomes used, and you'll quickly see "geanypathinclude: no such file or directory" on build. Unfortunately, waf does the opposite of pkg-config, replacing / with , so --prefix=/geany/path does not help. But the installation works, since it's done by waf, and the plugins don't care (AFAIK) what slashes are used on runtime.
BTW, the paths to Python are with \\ :)