The binary installer’s wheel files aren’t compatible with macOS El Capitan. The resulting snappyutil.log has:
INFO: Installing from Java module '/Users/snap/Applications/snap6/snap/modules/org-esa-snap-snap-python.jar'
INFO: Installing jpy...
ERROR: The module 'jpy' is required to run snappy, but no binary 'jpy' wheel matching the pattern
ERROR: 'jpy-{version}-cp27-{abi_tag}-macosx_10_11_x86_64.whl' could be found.
You can try to build a 'jpy' wheel yourself and then copy it into
"/Users/snap/.snap/snap-python/snappy" and then run the configuration again.
Please go to https://github.com/bcdev/jpy and follow the build instructions. E.g.
> git clone https://github.com/bcdev/jpy.git
> cd jpy
> python setup.py bdist_wheel
> cp dist/*.whl "/Users/snap/.snap/snap-python/snappy"
ERROR: Configuration failed
Since python setup.py install worked for jpy on your system, there is good
chance that python setup.py bdist_wheel also works.