Jeff,
I have a copy of the May 1915 The American Golfer that mentions Ross,
"Seaview has called in Donald Ross to build traps, and his ideas, together with those of Wilfred Reid, should stiffen the Absecon course considerably."
Seems that Wilson (likely with Flynn's assistance) and Reid were tossed in the historical dustbin in favor of Ross. Certainly the routing is the backbone of any design and influenced the placing of the hazards. It should be considered a Wilson design, unless Ross redesigned the course rather than added traps.
As for Pocono Manor, We know that Flynn designed at least ten holes, the current holes 7-16 which correspond to Flynn's holes 3-12 resulting in an 18 hole course. I wouldn't be surprised if he redesigned the existing holes.
As for quirk, it sure characterizes the steeply downhill 3rd hole. It is 77 yards today and was 115 yards in Flynn's plan. Does that mean it was a completely blind shot? I'm not sure.