In the fakeroot.in script, you have:

   LIB=lib@fakeroot_transformed@@DLSUFFIX@

This is not correct, because if you configure fakeroot with a configure
option like --program-prefix='xxxxx', then this will be converted into

   LIB=libxxxxxfakeroot.so

which is not right, and is not what the makefile installs (so running
fakeroot fails).  I think that the correct line in fakeroot.in is simply:

   LIB=libfakeroot@DLSUFFIX@

This is an unfortunate situation.  Because libtool doesn't respect the
transformation, the .so files are renamed in debian/rules, and this is
why the @fakeroot_transformed@ substitution is done.

The only better solution I can think of is to do as you say in the
upstream source and then carry a Debian-specific patch forever in
the package.

I'll think about this.