I don’t think it can be argued that the charge is ‘wrong’ in any meaningful way.
TfL publish two fares for travel between these stations and define the circumstances under which they’ll each be charged. Your journey matched one of those two sets of criteria so you were charged the fare that applies to that journey.
The fact that they also supply some textual commentary as to what the zonal assumptions behind the fares are is neither here nor there. A fare between A and B was quoted and that fare was charged.
To my knowledge National Rail fares don’t change based on diversionary routes, so why would TfLs?