On the previous version, X theme is using it's own image sizing for the thumbnails. Due to changes on Woocommerce 3.0 we move it back to it's original Woocommerce size. You can see the we put the following settings back:
We don't have plans yet as of the moment. I am not sure what you meant by this: By default X is treating the new WooCommerce 3.1.1 image thumbnails very poorly. because we don't have customization yet on that part. In case I missed something here, please clarify.