Carlyle,
I'm not going to give you any conspiracy theories of a mysterious par 3 between #13 & 14, (Insert here, emoticons of hilarious laughter) I'm just going to have to go off of my observation of the course. Pasatiempo is a BELOVED favorite of mine.
From my viewpoint, the entire Pasatiempo development is situated on a sort of huge but gradual hillside. This is one of the main features MacKenzie worked with when building the course; He also relied heavily on the arroyos that cut and dice the property. You image of #2 is an excellent example of this, and it is precisely what originally clued me to what was going with Pasatiempo, when I first played it in the late 1980's.
Just like a Redan-like green, the entire course is tilited from one high point #11 green/#12 tee to #2 green/#3 tee, and it is precisely the reason why when you are on the tee at #3, and you have all of these positive feelings of getting to the green with a certain club, and that it comes up a club and a half short everytime. Or at least it seems it!
In you images of #2, that back left pin position has been my death kneel everytime I have played it there. I have four-putted it twice!
Can you imagine playing Pasatiempo WITHOUT the use of red-white-or blue location flags for the green? Holes 1-4 alone would be really hard to read location-wise from the fairway! It really is all about deception there. The greens are located in the best spots, and as far as camoflauging, here is a perfect place to study the MacKenzie charm. They are placed perfectly in regards to the downhill slope in regards to vision.
(I hope I'm making sense.)
Yes, it maybe inundated with trees on some of the holes, especially since they were designed as shared fairways. (Holes 1&9; 2&3; 6&7; 10&17; 11&12 for example)
Tom's bunker work looks great, and it is an honor that we are allowed entry there to experience it all. Three cheers for Pasatiempo and the membership!