I could cite other examples as well where NYSDOT's engineers are very intractable, and act like they are always right even when presented with evidence to the contrary.
Engineers are very hesitant to do anything outside of guidelines. The instance I always fall back to was one here in Kentucky on the AA Highway. After a number of fatal wrecks at an intersection, local leaders and residents kept requesting a traffic light be installed. The intersection didn't meet warrants for a signal, so the request was always denied. But the Transportation Cabinet secretary at the time was not an engineer. After the locals approached him, he overrode the engineers and had the signal installed.
The best advice for the locals in this situation would be to take their case to the highest non-engineer who has jurisdiction over NYSDOT.
Engineers are legally responsible for their decisions.
You made my day. Was any DOT engineer legally prosecuted in recent history?
In particular, for the case @hbelkins mentioned - installing traffic light when it is not required (not on interstate or roundabout, I assume).
The problem I see is exactly the opposite - while such responsibility exists on the books, it is not applied - but management influence is very real. So, as
@SignBridge describes, engineers are doing things for the pleasure of management, population be damned. Flirting with forum limitations, I can add that this is not totally unlike issues with police.