What steps will reproduce the problem? 1. configure on 64-bit system w/o /usr/lib64 present
2. also, repeat with specifying correct LDD_FLAGS, etc. --> still no dice

What is the expected output? What do you see instead? configure should complete(all dependencies are installed) instead, install fails with: configure: error: Could not link against -lGLU ! configure: error: Could not link against -lGL ! configure can be made to pass the first failure by injecting appropriate flags.
however, then the latter results.

What version of the product are you using? On what operating system? Ubuntu 14.04, all of the dependencies installed I.A.W. INSTALL

Please provide any additional information below. I believe this stems from AX_CHECK_GL and AX_CHECK_GLU expecting 64-bit libs to be in /usr/lib64. It's common enough of an assumption that it's probably better to just add a note in the INSTALL file to the effect of :

If configure fails with the following message:
     configure: error: Could not link against -lGLU !
or:
     configure: error: Could not link against -lGL !

then check to ensure your O/S includes a /usr/lib64 directory 
for 64-bit libraries. If not, you may create a symlink to your 
distro's 64-bit libraries:
      cd /usr
      sudo ln -s <your distro's 64-bit libs fullpath> lib64 
for Ubuntu 14.04, for example, this would be 
      cd /usr
      sudo ln -s  /usr/lib/x86_64-linux-gnu/ lib64

Alternatively, you could add platform-awareness of lib64 location to the aforementioned checks. I have tried manually specifying the locations in invoking configure, but the flags don't seem to be applied until after the check is made, and I'm not savvy enough with auto-tools to grok what's happening.