The plugin cannot modify any snippets created by WooCommerce. However you can completely deactivate the generation of snippets created from it. Then you can re-create the products snippet on your own. In version 2.2 the plugin has almost full WooCommerce support. So it might be that you get in trouble by creating snippets for variable products with multiple prices, for example.
- Schema for WooCommerce: The ultimate Guide
- How to set up a Rich Snippet for WooCommerce products