expected behaviour of configure --prefix vs specialized install paths


I was wondering on what the proper behaviour should be for projects that
install specialized data/objects, including
- GConf schema files
- Bonobo components
- gdk pixbuf loaders
among others.

In my opinion any auto* project should be able to pass make distcheck. 
This means, among other things, that they shouldn't install stuff to
non-writable directories.

Now, on a clean distro, files that need to be picked up by
GConf/bonobo/gdk/... are mostly in /usr, and hence not writable.

So, projects can choose to either
a) autodetect these locations through the preferred mechanism (for
example using pkg-config to query for the right location)
b) honour the prefix specified (or not specified) by configure.

Which of these two is to be considered the right way of doing things ?
What do most projects use ? What drawbacks are there to either mechanism
? What workarounds are there for each receiving tool ? Am I missing some
other option ?

For example, for GConf it seems a lot of projects make schema
installation fail without warning so make distcheck can pass, which
makes sense since it's not really the installation of a file on the file
system.  Should the same be done for installation of the other types of
files ?


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