they do but not as much as PA1..for me if you want player individuality PA1 is the best without being totally assisted..now the dilemma is how much freedom you want? I have settled for PA1 with manual shooting as I get no satisfaction from shooting with the other methods. I can also always use the manual modifier which is true manual when needed.
There is absolutely no way that Konami have a built in mechanism that distinguishes between player stats when the human player is using manual controls. Player stats do not matter.