Even with Brown's underperformance, it's not like Whitman performed much better as a result. Kashkari only lost 0.8% of Whitman's support under the top-two system and Cox only lost 2.8% in a way worse environment for the GOP.
Also, I don't think it goes without saying, but the California midterm electorate can look very weird. I almost wanna say the 2018 cycle was an outlier in that regard.
The best performance for California Republicans since 1994 also seems to be in 2006 which was a dem wave year nationally so California may very well not have its results correlated to the national environment.