I haven't heard anything about those remains being identified as Negrete.
This case has haunted me for years because I was at UCLA when it happened. In fact, two years prior, I had lived in Dykstra Hall on the same floor he was living on when he disappeared. It just never made any sense.
Security in the dorms was tight. To get into any building, you had to have your student ID scanned and there were security cameras. There would no reason for anyone over, say, 21 to be near the dorms, especially because UCLA only guaranteed housing to freshmen at the time, so I'm not sure who the unidentified stranger they've talked about could have been. The bus stop his scent was tracked to was quite far; I'm going to guess almost a mile and mostly up a steep hill.
Other things to consider: UCLA is in a super fancy area; it's bordered by Bel Air, Westwood, and Holmby Hills (where the Playboy mansion and the Spelling estate were). While there is a notable homeless population in Westwood Village, the idea that one would have wondered that far out of the village and into the dorm area on the one night a kid went out in the middle of the night is very unlikely; I would say the same for someone trolling a victim. Why go to a campus with security at 4 am and hope you find someone walking around? There's also paid security driving around all of those adjoining neighborhoods 24 hours a day.
I know some previous posters said that the buried under the construction scenario is unlikely, but it's what I've always thought was the most likely scenario. There was an absurd amount of construction going on at the time; Dyksta didn't even have a dining hall or parking lot during the 97-98 school year (when I lived there) because they had been demolished for new construction. I don't if that had changed by 1999 or not, but I do know that much of the construction was around Dykstra and we were constantly having to take new detours and routes as the construction developed. I was recently on campus and the campus housing area was unrecognizable. That he could have fallen given the state of things during my time living there is not out of question. I don't know how construction people approach pouring cement, though.
The other thing I've wondered is if he might have been secretly gay (I'm not sure, but I believe his family is Catholic) and he had arranged to meet someone but didn't tell anyone in order to keep that a secret. Things were different then, and people weren't as accepting about that. Perhaps he was on some online site in the middle of the night and decided to get picked up by the wrong person? He was obviously computer savvy. I certainly don't want to spread rumors, but that is one of the few things I could think of that would account for how he would come to be picked up by a dangerous person at all.