The key word there is ‘similar’, with the question being how similar. While a UC 3.9 might well beat a CSU 3.9, it’s highly doubtful that a UC 3.5 would beat a CSU 3.9.
One simple reason is that the med-school rankings themselves do not differentiate amongst GPA’s from different schools. A med-school that admits ‘too many’ students with relatively low GPA’s from difficult schools such that its entire admitted class has a lower average GPA than other med-schools would be deemed by the ranking methodologies to be a (relatively) less selective med-school and would therefore have its ranking reduced. Med-school adcoms are not exactly delighted by the prospect of having to tell the Dean that the school’s ranking has declined. It’s safer to let sleeping dogs lie by simply admitting a slew of students with high GPA’s from easy schools so that nobody’s the wiser.