The bug number for dh-python is #949305. I don't see how the dh-python bug is blocking a fix here, so I'll leave setting the tag to you. In addition, if they decide to rank "cmake" higher than "distutils" (e.g. when sorting the plugins alphabetically), then your package will use the wrong toolchain all the time.
Adding a Build-Conflicts: would do the right thing, but might be a bit drastic. There seems to be another solution: pybuild supports "-s" or "--system" to select "distutils". Not sure how to make dh to pass arguments to pybuild ... But pybuild also supports the environment variable PYBUILD_SYSTEM. Just mentioning, I did not test that.
