The article mentions runway 4L was being used for takeoffs. In the ATC communications, you can hear them say "American 185, runway 31L at KE, line up and wait" before telling Delta 1943 to cancel their takeoff clearance. And after the near collision, ATC tells American 106 Heavy "we're departing runway 4L."
Wouldn't the line up and wait call for American 185 mean that they were departing from both 4L and 31L?
They were landing 4R and 4L, departing 4L and 31L at KE. American 106 ended up departing 31L full length since that's where they had decided to taxi to and it was probably easier to just get rid of them that way rather than have them cross 4L again to depart where everyone else was departing from.
Departing 4L mean that there are no 31L full length take-off (except very very heavy aircraft). 31L at KE does not conflict with 4L, nor does it require crossing 4L.
Wouldn't the line up and wait call for American 185 mean that they were departing from both 4L and 31L?