I think also (to expand on what Clem said) only 6 car trains can fit into Flatbush Ave. Terminal (Please correct me if I'm mistaken about that) So it makes sense to run those 6 car trains to the branches with the lower ridership where you don't need 8-10-12 car trains anyway.
In fact I read somewhere that Pennsy actually designed the Jamaica complex with this in mind and the straight moves that Clem mentioned.
If you look at the eastbound arrangement track 8 (from Penn Sta.) is oriented to the main-line. Track 7 (from Penn Sta.) to the Montauk (Babylon) branch. And Track 6 coming off Atlantic Ave. to the "fly-under" to the Atlantic Branch.
The same is true westbound if you look at how the tracks from the Main, Montauk, and Atlantic Branches come in to Station Tracks 1-2-3 which are roughly aligned to the 2 Penn Sta. tracks and the route to Atlantic Ave. The story also pointed out that it is not generally known or appreciated how smart the original designers of the Pennsy-Long Island RR were back in the early 20th Century when they planned and built all of this. When the usual sequence of arriving trains works as intended, none of the 2 or 3 trains will have to cross in front of another, as the 3 routes run parallel to each other.