More info I found today (reading over at the railroad.net forum):
At least some of the Amtrak engineers getting qualified on this territory did so as far back as February/March. And the trips they made were still "at slow freight speeds" on the old branch (which I will guess at the time was not yet finished with the rebuilding for passenger service). As such, they may not have had many (any?) trips over the newly-opened line at passenger operating speeds (which would necessitate learning braking points for the slowdown).
(this is what someone in that forum posted, can't vouch for its veracity, but sounds plausible)
The "positive train control" was still in the process of being installed and probably wasn't going to be ready until June 2018. Again, takes months and months to get these systems up-and-running reliably. Much fine-tuning involved.
The NTSB has video from inside the cab immediately prior to the accident. The tape shows no cellphone usage, so that's not a factor. The engineer apparently made some comment about excessive speed immediately prior to the derailment. The video ends with the locomotive going 78mph. It's possible there is more video from the "forward-facing" camera, but nothing to report on it yet.
Amtrak will resume running the service on the previously-used route (BNSF) and won't attempt to run over this bypass again until the PTC system is operational.
The title of the article is b.s.
There don't need to be thousands of "unanswered questions" as to what caused this.
Obviously, the derailment was from excessive speed due to the failure to control train speed for conditions and restrictions.
Specific questions I would ask at the investigation:
1. How long since the engineer qualified?
2. Had he made qualifying trips over the line at passenger speeds?
3. If so, how many trips? Any at night (in the dark)?
4. Did anyone in a supervisory position ride with him for a "check ride"?
Chances are, the guy running the train thought to himself that "he was ready", and then found out to his surprise, that maybe he wasn't...