Peter Martin said:
An article celebrating the centennial of SR in a 2005 issue of “Discover” Magazine
Fyi, this would probably not be an acceptable source here on PF; we want to see textbooks or peer-reviewed papers. The moderators would have to look at it to make a determination.
That said, your criticism of the article's argument is incorrect; the argument, at least as you present it here, is wrong, but not for the reason you give. See below.
Peter Martin said:
Had the conductor flashed the light backward with respect to the train’s motion, the forward-moving rear of the car would have intercepted the oncoming light sooner than it would have were the train motionless on the tracks.
Yes; and what this demonstrates is relativity of simultaneity.
Peter Martin said:
In this case, the trackside observer would see the light taking a shorter time for the experiment, and would interpret the train’s “clock” as running “too fast”
No, he would interpret it as relativity of simultaneity: light beams which would reach the ends of a motionless train simultaneously--or, equivalently, would reach the points on the track which would mark the ends of a motionless train simultaneously--do not reach the ends of a moving train simultaneously.
So a proper criticism of the argument, at least as you are presenting it here, is that the experiment is not about time dilation at all; it's about relativity of simultaneity. Neither the "forward" nor the "reverse" aspects of the scenario have anything to do with time dilation. To demonstrate time dilation, you would need a light pulse that goes out and comes back, as in a light clock, or some equivalent way of comparing clock rates.
To know whether the actual article is in fact making this mistake, I would have to see the article itself. It's quite possible that it is, since Discover magazine is not exactly a gold-plated source for relativity physics; but it's also possible that you are misinterpreting the argument given in the actual article.