Firstly, if you look at the compiler output you pasted very carefully, you'll notice that the compilation and linkage of the dedicated server actually succeeded so you ought to find a working oa_ded.x86_64 in your build/release-linux-x86_64/ directory.
Secondly, I've got the 64-bit compilation of the client working too, so if you're still interested:
The size_t definition in the SDL_config_minimal.h header really is wrong for 64 bit, so you'll have to open code/SDL12/include/SDL_config_minimal.h with a text editor and change line 38 into:
typedef unsigned long int size_t;
Finally, you could have missing dependencies (some mesa, libvorbisfile and SDL stuff for me), so you might get errors on those (in which case you'll have to install those missing development packages).
Edit: no autoconfig at all
