I don't think LLL was ever winning Screenplay, not since Manchester got those raves at Sundance. Still think it has a pretty strong grip on Director and Picture, as well as some techs (Cinematography, PD, CD, Editing and Song are all plausible/achievable) and maybe Actress if everything goes right. It's true that we can look back on Boyhood and TSN as seemingly obvious winners but LLL really does have more going for it.
Not exactly shocked NBR didn't go for it either. It, Manchester and Moonlight have a similar level of acclaim, and you'd expect some critics to simply like the latter two more and/or lean towards the independent underdog character dramas rather than the lavish Hollywood production they figure will almost certainly clean the big awards anyway. If it somehow continues to not win anything big anywhere for the first half of December I guess that might be a slight cause for alarm.