Actually, the puck should have the ability to swing in far enough to protrude a little like what you're seeing there. Think about how NOT tight the seal would be if it only came even with the flange, or even worse, not quite even with the flange??
You'll notice the puck is hinged its self, so that if you push it down even with the flange it still has the ability to remain parallel with the flange.
All downpipes of this design should have the ability for the puck to protrude a little just like that.
What do you mean the puck wont close all the way? Isn't the puck its self hinged where it mounts? It should swivel a little.
Now, as far as the flange being flat, well that's a different issue, that may need attention.
I run a THDP, I've had it off quite a few times lately for various resons. You should see how far the puck can protrude on a good high quality pipe like this one!
You just need to make sure the puck is large enough to cover the hole, and allows for some "hole massaging" in case you need to increase the hole size for better boost control.
Smear some grease or something similar on the puck face, test fit the pipe, notice the pattern left on the turbine housing after removal.