TfL takes train frequency into account when deciding zonal coverage. Streatham has frequent northbound trains on Thameslink and Southern, whereas from Tooting you are stuck with the Wimbledon loop of the Thameslink line which is half hourly. This explains the different treatment. Note that Streatham to Southfields is Zone 3 only, so East Putney is the cut point.
TfL only need half an excuse to default to a Zone 1 route and in this case the Zone 1 competitor would be via Herne Hill and Victoria. You may well ask why TfL assume that a transfer at Victoria happened when no touches at the Victoria gateline took place, but there are lots of examples of TfL not distinguishing routes based on Out of Station Interchanges where they could do, especially where a pink reader exists to prove the cheaper route instead.
