Hey Kanos - do you have a close up of the rear strut piston? From your pic, it seems like the rears do have that little shoulder as well. And they actually look pretty identical in size. I would think that it has to have it and be the same size as there are no differences between the Group N hats and stock hats except for the rubber durometer. And no difference between the hats that go on the inverted struts and the OEM struts. Know what I mean?
The knocking we had, sorry if I wasn't clear, was on STI V7 RA Spec C struts with 04 STi Pink springs and 04STi Group N hats. This was not on OEM struts. I only have the OEM struts pictured as they are the only one's I had access to at the time. As I was saying above, I can't imagine there would be a difference between the inverted and the OEM at that threaded end of the piston.
If you have a chance, get your car up on jackstands and then with the wheel off (so you can see up there) jack up the rear hub and see if the strut has play going into the hat. Ours did, despite numerous attempts at retightening the 17mm nut at the hat (with an impact wrench).
Maybe I'm jumping the gun here and am wrong but it seems like the answer.