Yeah, I think this is most likelyI suspect that the ticket is to Stratford because Advance tickets to Liverpool Street were 'sold out' but were still available to Stratford and so it is a far cheaper option. Happens to me frequently with 'near the date of travel' bookings for Norwich - London.
Likely because the GA trains will be reservable, and therefore must have the relevant advance quota even for that short hop, which is unlikely. Tube or EL aren't reservable so are fine.Why the journey planner then chooses the EL rather than G.Anglia for the Stratford-Liverpool St leg, who knows.