If your requirement is to customize the buttons only for this section then you can hide the Default buttons of the FlowAction(this will hide all three buttons Cancel,Save,Submit). To hide the default buttons- Open Flow Action> Action tab> Enable the check box "Hide the default action section buttons"
Now you can have a button(that performs submit) in your section. For this you can have Finish assignment action configured on your button. If you further want to show a Pop up on click on this button you can launch a FA on click of the button and lastly finish assignment.
Please let me know if you have any queries or if my understanding is wrong.