Hi Jase,
I’ve split this question as it really is a new topic.
You are correct that both legs of your journey approach Stratford from the zone 3 side, but you do need to pay for zone 3. Therefore you need a zone 3-6 travelcard to make that journey without issue. Having said that, if you do try to make the journey with an Oyster card with a zone 4-6 travelcard, the system will deduct a zone 3 single fare from your PAYG balance. You only have a problem if you haven’t got enough balance to pay for that fare.