In addition to the good points mentioned above, let me add a few additional thoughts on why putting stats are higher at Torrey ... I played last Tuesday and have played the day before the tournament a few times ...
1) For the South Course, the greens are quite good early in the day, but they seem to become worse faster than other greens I've played. 2) It doesn't rain much in San Diego, except the week leading-up to the Farmers it seems. I think the rain may contribute to 1) above and also to 3) 3) Because the rough always seems to be heavier than planned / expected, it's hard to chip closer on missed greens ... there might be more chips that wind-up closer to 7-10 feet than 5-8 feet ... which may lead to worse putting stats. (I don't have data, but this seems to be the case when I watch my foursome and our pros). 4) There are two courses so the pros have to spread out their time ... and 5) The start is now on Wednesday which also reduces practice time and getting to know the greens a little. 6) For the North Course, the transition is just tough ... I don't know if they can do any thing else. 7) The field may be weaker - I think some do skip because it's a public course with poa greens, but I do think a lot come because they like the area and/or they are in the US or from far away and they might as well play since they can get in the tournament.
I do have to say that the course has been in pretty good shape in the summer. Also, I was surprised at how good the greens were on the South Course at 6:40 am the first time I played the day before the tournament.