We are currently out of the 2-6S backup BEC for Pixhawk 2, which you would likely need as pat of your kit. We will have them in stock in two weeks.
Not sure about Li-Ion but as long as the battery is within the voltage limit, I don’t think there should be a problem. You can ask the manufacturer directly if you would like to make sure: http://www.mauch-electronic.com/contact
Without backup BEC, this is the kit you would want: