Here's my take. I'm willing to bet the pilots were all prepped up to takeoff on 31L as they were using both 4L and 31L at intersection KE. Aircraft departing 4L will cross 31L at K, crossing behind departing aircraft on 31L. During preflight, we usually have a good idea to which runway we are using for takeoff, but sometimes it changes between then and the taxi out. I'm not sure if the runway configuration changed during this time though. So they probably had a 31L (full length) departure engrained in their heads then entire time. So now we have expectation bias. On taxi out, the FO did not read back the runway assignment. The ground controller didn't confirm it either. Then, when they got the clearance to cross 31L, she just rattled it off, probably because that was in their head of what they were going to do. Have you ever repeated something back without even deciphering what was said, and then you go "wait, what did you say again?" (my wife says I do that).
As to the controller not saying turn right on K and cross 31L...Yeah, I thought of that too. My controller friend said they don't have to give directions so it wasn't required. Perhaps the NTSB should recommend directions for this sort of thing? Maybe they will.