Getting LLVM/Clang to be 16 bit aligned
According to clang's sources, it does support mac68k alignment rules. It seems that right now you can enable it via "#pragma options align=mac68k" only. If you're ok with small clang hacking, then you can implement the cmdline option as well and submit the patch to clang.
I would suggest looking at #pragma pack (see http://msdn.microsoft.com/en-us/library/2e70t5y1%28v=vs.80%29.aspx and http://gcc.gnu.org/onlinedocs/gcc/Structure_002dPacking-Pragmas.html). It's relatively easy to use, and should work with any compiler Apple ships.
i use the latest gcc/gortran on osx compiled by the guys at ibm, if you read the gcc manual there are at least 8 different alignment optimizations to consider not just the bulk malign