I used a National Railcard discounted Oyster card with Zones 1-2 Travelcard loaded. My journey was Willesden Green – West Hampstead – Hackney Central – Chingford off-peak.
The fare charged was £1.25. However a standalone fare for a Zones 3-5 journey on the same scale (Clapton – Chingford) is £1.45.
There are fewer scales when it comes to extension fares, so you’ve been charged at the TfL-LU rate. You’d only be charged more if the journey was on the NR or NR-T scales.
Sorry for the delay replying. I don’t know for certain, but I’d expect in this case that the additional premium would apply. If you make the journey, perhas you could let us know.