I've only done a couple unemployment exclusions so far since the forms release in ProSeries and I have not seen them make the adjustment automatically for Calif. It was carrying over the Federal AGI (already reduced due to Sch. 1, line 8 UCE), then in the 540CA, it was subtracting it again as it usually does. It would not affect Social Security since California does not tax social security.
If you mean the Federal return, yes, I am letting the program do all the work.