According to
THIS site the same thing is true of CA toll bridges, so it shouldn't come as any big surprise.
Using the Benicia-Martinez Bridge as an example, the regular toll for a four axle vehicle is $5.00, however if you're towing they count the total number of axles on the roadway, and charge $5.00 per axle. So for a non-tag coach and toad the total toll would be $20.00 compared to a total of $10.00 if each vehicle were driven separately.
Personally it would be a waste of my time to consider unhooking and driving each vehicle separately, even if there was a safe place to do so.