"The current scheduled departures shows some interesting conflicts. Assuming that the travel time from Queens Plaza via the 11th St Connector is roughly the same time as it takes trains from Queensboro Plaza to reach the merge point."
I noticed that, too, and as a result of Mr. Bauman's pointing it out I did some investigating. In the AM rush, the running time from Queensboro Plaza to (leaving) Lexington Avenue on the N is a flat 5 minutes, of which 3-1/2 minutes is from 11th Street Tower to (leaving) Lexington Avenue. Strangely, running times from Queens Plaza to (leaving) Lexington Avenue via the R, and from Queensboro Plaza to (leaving) Lexington Avenue via the W, vary during the AM rush, almost from trip to trip.
It looks as if things are hammered out at 11th Street Tower (which isn't listed on the R or W timetables, only the N) by holding R or W trains.
David