Mitch,
I used to live in San Francisco and therefore am lucky to have a couple of pals who are members. I was not aware the design was originally Graves, but your post prompted a Google search, which turned up several guide listings attributing it to Graves. I have never heard of a MacKenzie connection.
Graves also worked on Sonoma Golf Club, one of my favorites in Northern California, and the Sea Ranch Links. Like Lake Merced, both have interesting routings, lots of variety in the holes, and strategic interest. I think Lake Merced is much better than Harding, but I haven't played the latter recently. The OClub and SFGC are each in a class all their own, but I like your suggestion that there are "San Francisco holes." The Lake, the Pacific Ocean, the sandy topography, and the wind all influence play on these courses.
The work at Lake Merced by Jones was done 6-7? years ago. I thought the course improved (and was made more difficult), and I like the new bunkering, but some members will quibble. I thoroughly enjoy it, and on my last visit in October, the maintenance philosophy seemed to reflect a preference for "fast and firm"--which I thought was great, but which again I understand some members are not thrilled with.