The rider already explained what happened, it's on cyclingnews front page.The only thing I'm contrary with is the notion that WvA should have given the motorbike a wider berth, for the first reason on your list (as I too have stressed). That error to me trumps all the rest. The riders have priority, not the motorbikes, and when it comes to chosing the best line it is their prerogative. In this case the motorbike was on the right where that best line was, not to mention he should have been way further ahead/away and above all not there in that moment. Plus it caused Alaphilippe to "have to look out for something", he shouldn't have had to do.
They had gainned more then 20 seconds to the peloton, so the motos had to let the riders pass. He went to the right and slowed down so they could do that.
IMO they had plenty of space to go around the motorbike in safety and they are not morons. They know and understand when a bike is letting them pass. They still chose to be very close to it. Unfortunately Alaphillipe was not paying attention.
It was just an unfortunate incident.