you seem to misunderstand how the dynamic linker works. There is no need for an 
debian/ubuntu specific configuration (beyond maybe locating X11)
An application must only link against what it *directly* uses.
fltk needs X11, program X needs fltk, then X does *not* need to link against X11
this is different when X uses fltk *and* X11 directly (as apparently the case 
in your app), then it *must* link against both directly and not rely on 
indirect linkage.

for why indirect linkage is bad beyond distributions internals:
library B is linked against C
A uses symbols from C and B but only links against B, this works as the 
dependency is satisfied indirectly through B
not B refactors its code and does not need C anymore
A is now broken as it still needs C but the indirect dependency is not there 
anymore.

solution: link A against what its needs, namely B *and* C

> X11, Xft, fontconfig and jpeg/png libraries:  what is complicated here
(as obviously 99% of UI apps relies on this).

only very few have a direct dependency on X11, the dependency is
satisfied indirectly in pretty much all cases.

> Dynamic linker knows nothing if there are missing symbols and unless
> compiler is provided with needed shared library. Also, we are not
> using libtool (yet) so there are no .la files to resolve dependencies.

there are no missing symbols in proper shared libraries, so there is no problem.
If there are symbols missing its a bug, but its not the case for fltk.

Also it might shock you to hear, la files are not the "solution", debian 
removes these too for the exact same reason fltk is patched.
You must never rely on dependency_libs of la files being filed.
http://wiki.debian.org/ReleaseGoals/LAFileRemoval

** Changed in: fltk1.3 (Ubuntu)
       Status: New => Opinion

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https://bugs.launchpad.net/bugs/1007429

Title:
  FLTK fltk-config tool is broken

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