synfig should know, where it's libs were installed.

I have straced synfig with the benchmark file. There i see, that the libs were not easy to find for synfig. It searches on my computer in 3 folders, before it finds what it wants.

Could the position of these files be put in a configuration file, which get read once at startup?

Actually, those paths are correct. Synfig was designed around the idea of being modular, you can build external modules, put them in any of the paths used and use them. By searching the extra paths you get an opportunity to override the built-in modules with your custom versions. They enable you to have custom modules associated with a specific project, with all projects for a specific user or load the one built out of the source tree.

Only the last two paths really need to be improved/changed - need to support relocatable binaries as Windows and MacOS X need that to work best. Patches welcome for that, we need more developers.