I would imagine its a mixture of capacity and pathing that has dictated that those 2 ex-Reading trains call additionally at Acton instead of an ex Heathrow T5 train. Those 2 ex-Reading trains are odd enough in that they run non stop between West Drayton and Ealing, mirroring the GWR services they replaced.
Indeed, you'd think an earlier direct GEML to Heathrow train would be desired by GEML lizzy line passengers. Pure speculation but running the train empty from Gidea Park and first entering passenger service at Stratford might be motivated by a desire to retain flexibilty of the origin of the unit, so that it could come from Ilford depot vice Gidea Park if necessary. I note that the 0639 from Whitechapel on a Saturday remains unchanged.
And it would appear there is a corresponding service at 0014 from Paddington which only runs to Whitechapel before running empty to Gidea Park sidings, which is perhaps odder given the shorter nature and i would have thought there'd be a reluctance to terminate services in the core, given the increased potential for knock on delays.