If you're using the "install GCC" option, you still need to link libgomp to the directory that 3dAllineate wants it to be in. Something like this should work:
ln -s /usr/local/Cellar/gcc/5.2.0/lib/gcc/5/libgomp.1.dylib /usr/local/lib/libgomp.1.dylib
Though make sure that the file really exists. If you don't see it, verify that you installed GCC with the "--with-all-languages" option from homebrew.
Those variables being blank is normal with this option. The SIP (among other things) disables a sub-environment (like Python) from being able to read (or write) DYLD variables.