The free bus area pre-dates the free tube by several years, so there's some kind of 'history' response in there. More importantly though they are designed to serve different markets: the bus allows staff working at several around-LHR sites to access commuter facilities (e.g. Hatton Cross, which you'll remember only needs a Z5 travelcard) and therefore fewer choose to drive to work and congest the airport perimeter. The inter-terminal-transfer is designed for passengers to move around easily - there's less need for them to go to Hatton Cross so it's not offered - for those who do want to, TfL can collect the fare.

The X26 is exempted because the operators are trying to maintain the 'express' nature and keep it to through- rather than local-journeys. Similarly, the 81 and 90 routes are not part of the 'free flow' zone despite having routes that could make sense, because they don't want to interrupt through journeys too much.