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.
No doubt ascribed to passengers holding doors or not moving quickly enough on these trains. :-)
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.
Holding trains between stations is not productive for moving passengers. If trains have to be held, due to unbalanced merges, they should be held in stations where the time could be used for passenger loading.
There should be no merging conflicts, if the schedule is properly drawn. The unequal travel times is one tipoff that something is amiss. One way to avoid merging conflicts is to start at the merge point and work backwards. It's amusing that the 11th St Tower is listed in one schedule and not the others.
The routing is a little more complex. The W merges with the Q's at 57th. Have they scheduled any conflicts there? What about the N merging with the W at DeKalb, the N and R merging with the M south of Whitehall and the W and M merging at 9th Ave? No wonder the TA refuses to publish a complete schedule - they're afraid their scheduling expertise would be exposed. :-)