The aviation industry doesn't usually reduce incidents down to a single proximate or ultimate cause like that, but instead notes every decision/event that contributed to the incident occurring. And then they usually spend time on how they can reduce the likelihood of such an event reoccurring at every single point in that chain. It appears that the coast guard plane lined up on the runway to prepare for takeoff instead of holding short of the runway as instructed and the JAL pilots did not see that their runway was not actually clear until it was too late to avoid a collision (if they saw the other plane at all).
From the JAL plane's perspective, automation is only as good as the sensors and logic which would be checking for if a runway is actually clear. Regardless of whether extant solutions are better than humans right now or will be better in the future, those solutions will still have a same failure mode as humans, which is suddenly realizing a runway that appeared to be clear actually isn't clear when it is too late to abort.
From the coast guard plane's perspective and from the controller perspective, automation and warnings might have been able to alert or prevent, however, automation can't just be thrown around as a solution without deep knowledge of the system and environment in which it will work. The main reason for this is ensuring that the transition between automated-control and human-control is clearly evident to the humans involved, that it occurs with enough time for the human to actually be able to avert a problem, and that the human is actually ready to take control. If the automated system silently disengages, a plane with permission to take off from a runway will instead just sit on the runway because the pilot assumes the automation will begin takeoff as expected, which brings us right back to a plane on the runway when it shouldn't be there and a landing plane not seeing it until it is too late. It is actually possible to land a plane purely with automation (military drones do it all the time), however that isn't done on commercial aircraft, because the constraints are so tight that if the automation were to fail for any reason there is a large chance the human pilot would be unable to prevent a crash even when perfectly monitoring the system (and perfect monitoring can't be assumed).