it would appear that in the Japanese collision, the pilot may have gone onto the runway with the misapprehension that given his taxiing instruction including "number 1" meaning number 1 to use the runway having not been on frequency when JL516 got its landing clearance. Doesn't explain why they would turn off a taxiway onto the runway when not cleared to do that. It also needs to be established how easy it is to see holding points if the taxiway stop bars were out of action which appears to be been put in a Notam.
With it being on the runway for 40 seconds, I wondered what would be the distance the JAL aircraft would have been at when the DHC8 entered the runway,. Not knowing the approach speed but guessing it would be 140 to 150 knots, I would say JAL was around 2 miles out. I am not that sure that they would have seen anything on the runway apart from lights and no discernible aircraft as whatever lights the DHC8 had may have blended into the runway lights.
The other thing that strikes me is the transcript looks like JL516 was cleared to land only once. I'm wondering if from a safety standpoint whether there should be (a) reconfirmation of a landing clearance when an aircraft is 2 miles out, or (b) when a departing aircraft contacts the tower frequency whether an advisory should included y the controller in giving taxiing instructions along the lines of "Landing traffic 2 miles", especially if you have not spoken to the landing traffic after a other aircraft have contacted you. Maybe a 3rd option would be to do a general broadcast of "landing traffic 2 miles" by the controller without referring it to a given aircraft so that all aircraft and/or vehicles on frequency on the ground will be aware not to encroach onto the runway.