A good CFI will beat you up with his rolled news paper if he notices your MSFS training 
- I told my CFI when I started that I had flown with FS for about 16 years when we sat down to discuss the first flight. He said ok…then you get to do everything as if I wasn’t even there and I will only step in if I don’t think it is going to end well.
We did the preflight…where he did mention a few things he wanted to see, that the Piper checklist was a bit vague on and he did have to show the engine fuel strainer function since that was a odd one and since I did not see immediately how it worked I rather asked before breaking one of Judy Scholl’s airplanes 
Then we started her up, and he was stumped because I got the by the little Piper trick on the starter where you go from BOTH mags to start by pushing into the panel a little.
Taxi and runup no issue and also the Takeoff was without any action on his part. We flew a full pattern but he told me ahead that he would want to go around relatively soon after turning final. This was just to establish the pattern, aircraft control and the GO-around on his command.
On the second pattern I landed and taxied off the active. We did a few more that day and he never once touched the controls.
So I don’t think FS is as bad as all that… BUT certain things you will not learn with FS and some things you do learn are not always helpful.
In the real airplane you actually use visual cues outside, and seat of the pants as well as your ears a lot more than in FS.
FS in some ways forces you to rely more on the gauges to judge the flight than you would otherwise. That is maybe the hardest thing if you are going from one to the other.
In FS9 and FSX I had modified the simulated airplanes to match the real world airplanes performance for Warrior, Archer and Saratoga. Even fuel flow was accurate to a few tenth of a gallon. That is unfortunately that sort of fine tuning is beyond my skills with MSFS.
So I am just flying the aircraft I get from the store or from very talented Moders 