"Your anecdotal evidence is contrary to my own experiences during the 1954-1959 period, when I too regularly rode both the Flushing and E/F lines. "
Actually it is not.
"I must confess that I too thought that the motormen passed red signals on their approach to Main St from looking out the front window. However, I'd also occasionally look out the front door during the winter months. I'd see that the aspect had changed just before the train moved from the color of the signal light's glow."
This does not make that the rule. Your observations are too haphazard here and Victor's outline of why these events happen make sense.
"Looking out the front window had obscured a clear view of the signal because the motormen pulled even with it. I could not see the aspect change because the train body blocked a view of the signal and the beam. "
The only thing we can conclude here is that you observed very little at all. If you can produce a motorman from that era who can explain his procedures, then your story would gain credibility. As it stands, you appear to be fabricating.