I think all the removal and reinstallations warped the stock flange for me.
I tried to sand down the flange and found that only the outside edge of the flange showed scuff marks - the center hole + good 2mm around it was untouched by the sandpaper.
A unique advantage of this system is that you can easily remove the flex hose with a 14mm wrench and move it out of the way.
With the stock hard pipe, you kinda have to bend it slightly to get the turbo out.
-Ted