Hi Xan,
I have not tested the new configure script with Mac systems using CUDA - mine uses OpenCL only.
It seems to me that the problem is that the configure detects a Mac system and defaults to the OpenCL configuration for the AMD-based platforms.
Unfortunately I cannot test this at this moment. If you want to get your hands dirty, it should be easy to modify the
configure.ac for your particular case, forcing the libcuda rather than the libocl when building the final steps. It could also work if you disable the OpenCL library (i.e do not add --enable-ocl).
Sorry that I cannot be of more help!