Funny how stories like this come up when you've been thinking about this only a few days before..
There's a set of traffic lights installed only a few years ago on a national speed limit dual carriageway on the A617 near Mansfield, it's a fast road section where doing the NSL is perfectly safe for all but one section; the aforementioned traffic lights are at the bottom of a downhill run and partially obscured by trees.
There's a point when approaching these lights at NSL that, if they change, there isn't enough time at amber to stop safely for the red. Some people simply sail through the red, others have let tyre smoke out trying to stop in time.
I acknowledge that the best practice should be to slow down as soon as you see the lights, but let's be honest very few people do that. If the amber on those lights was increased to 4.5 seconds, I heartily believe that this junction would be much safer.
TL;DR, amber times should factor in the time to stop based on the road speed and conditions.