I think shaft flex does make a difference. What tends to be overblown in golf equipment is what a certain kind of shaft can do for your shots. Once you're in the right flex, the kind of shaft is only going to help so much.
I was talking with a fitter a few months ago and he said there is no such thing as a "low spin" shaft. It has to do with how the shaft feels to the golfer and how the golfer responds to the feel to change the shot data. I don't know if that's 100% but I think a big part of finding the right shaft is how the golfer "responds" to the shaft and head combo. Some players like there to some "play" in the shaft while other want it to feel boardy so they can swing hard and not have it go left. Again we're talking about feel and not what really happens or what really causes things to happen.
This video illustrates shaft flex, swing speed and the influence on creating club head speed.
My putting has improved leaps and bounds since getting fit with an EVNROLL putter. Got the ER3. Everyone is different. All i know is that is works for me. That said, if you cannot put the ball on the correct line, club face square, etc., just like anything else in the bag, does not matter what you get you are not going to get the results you want.