My theory, and that's all it really is, seems to fit fairly nicely with the facts that
are known.
For instance, it's known that a nine-hole course was built in 1907 by a "local engineer", and that demand was such that a second nine was built in 1908, purportedly by Willie Park. I know believe this is probably in error.
It's also known from Bob's research that J.Wood Platt wrote Mr. Gimbel something about "the new Willie Park course" in the 20s, although it would help to get a specific year.
We also know that the Gordons did work to both courses in the 50s to accommodate a driving range.
This is what I think happened;
The original 18 holes were probably built by the local engineer and possibly the addition was done by members, not Park. It may have not even occupied the exact same ground as the present South Course.
However, in the 1920's Park was brought in to either revamp the existing course, or build a complete new one. My guess is that this course may have included some of the holes that are now on the North course, and I'd speculate them to possibly be 1, 2, 9, 10, 18, none of which look much like Flynn. Park likely also built or revised holes at that time that are today occupied by the driving range.
At the end of the day, there was probably 18, or possibly 27 holes.
Then, at some later point I think Flynn added at least 9 holes and possibly 18, reconfiguring the other course in the process. I'd be really surprised to hear that the holes in the mid sections of each nine on the North Course (on the furthest points of the property) are not Flynn.
Then, the Gordon's came in the 50s and with the building of the driving range, added two brand new holes (12 & 13 of the South Course), and reconfigured others, including #3 & #18 of the South. They may have done other work, as well, and are also attributed with some unknown changes on the North course at that same time by Cornish & Whitten.
Feel free to shoot holes in this theory, but I think it has some merit for consideration.
But, I'd be VERY interested to see what the Hagley museum has for Philmont as well as the years involved.