Matt,
Thanks for posting this up.
Lake Chabot is certainly one of the quirkiest courses I've ever played, with the drop shot 9th, hitting back and forth over the road on 2-5,11 and then the bonkers 18th. I really enjoyed the latter part of the course where (at least back when I regularly played it in the late 90s) you had some spectacular views on 14 and 15.
Based on Google Earth elevation measurements, its looks like the changes might have been for the better. (even if the new 12 is a bit tight). With the old configuration, 15 played approx. 100 feet down the hill on 15, and then more than 100 feet back up the hill to 16 green.
With the current config you play over that canyon with the tee shot on 16 with typically only a short wedge flip to the green, (which appears to be roughly in the same spot as the prior one).
P.S. One of my fave holes on the course was 10, really loved how it curved thru that section with the side of the hill on the right.