3DF Zephyr Pro and 3DF Zephyr Aerial both offer a great batch tool you can control directly from Zephyr which can be accessed from the "Utilities" menu.
If you need to run reconstructions from the command line, you may be interested to our FlowEngine SDK - a fully featured C++ SDK built on the very same technology that powers 3DF Zephyr. Command line processing is not offered by 3DF Zephyr.