I searched a bit around but did not find a mention or a solution to this. If this is currently not possible, what options do we have to create grouped metaboxes programmatically so end user can then easily edit from backend?
In the array of parameter sent to the server, add a field meta_box to store all custom fields' values, including groups.
Put array of group's value into the meta_box field. Remember to format the group value properly, e.g. an array of sub-field's value. In short, send the data in the format when you click the Publish button in the frontend.
Then the plugin will handle the rest and update the post with correct value.