I assume because they wanted to take as much advantage of the highway right of way as they could, at Jamaica the Airtrain elevated is perpendicular to the Long Island Railroad and E and J subway, then makes a 90 degree right turn to the east to run elevated into stub end platforms, pointing away from Manhatten, on the south side of Jamaica LIRR station. In my opinion it's a rather long walk from the subway up to street or railroad mezzanine level, then under or over all the railroad tracks, then up, or down, to the airtrain concourse, then another long walk to get to the airtrain platforms, which for some reason are still about a block away from the pathway from the subway or railroad waiting room.
The airtain approach to Jamaica is similar to Newark aiport's airtrain, which comes from the airport perpendicular to the North East Corridor and makes a right turn to its platforms next to the North East Corridor's EWR station, except at EWR the airtrain's facing towards Newark, and stops just about where there's a straight passage to escalators and elevators to a mezzanine that goes directly to the railroad escalators and elevators.
Unless they build some new track that branches off somewhere south of Jamaica and then makes a big left turn, to serve Jamaica and continue on to Manhatten would require changing ends. Not that that should be a big deal with the current automated train operation, or even subway style operation, but it could be burdensome if they run under FRA railroad style operation, which always seems to me to involve a 30 minute brake test every time they change ends:)