Speed and space.
Frontier Yard in Buffalo is small by modern standards; and (especially since the shutdown of Seneca Yard) always packed. There's no room at the inn...
Entering a yard must be done at restricted speed, no more than 10 mph. Getting a two-mile train in and out at that speed can take some time.
It's more work for the dispatcher to line trains into the yard, coordinate traffic behind the yarding train, and then feed that train back into the traffic flow, than it is to just stop it, frequently for less than three minutes, on the main.
In addition, going into the yard brings the train no closer to the recrew. The yard parallels the main; getting the recrew to the train is actually easier on the mainline.
The same is done at Collinwood and Willard with through trains. At Collinwood, all trains (with rare exceptions) fuel...and the fueling stations are on the main tracks. The main runs right by the crew building...
Same at Willard. The recrew just walks outside, about 150 feet, to the main to change crews.