When I heard the clunking noise after first installing my v7 struts and 04 springs I had someone ride in the back and look at the strut top mounts to see if the strut was sliding up and down. They said they saw it move up a bit when going over bumps and stuff. Maybe this is what you experienced and saw when you jacked up your hub. When we felt that one big nut on the strut where the top hat is, it was very loose. My guess is once the rear suspension is compressed as when sitting on all fours, that 1/4-1/2 inch lip at the threaded part moved up into the strut top hat and then the thicker part of the sturt piston rested where it was supposed to on bottom of the strut top hat. So once we tightened the bolts again it solved the problem.
I think the added weight of the car pushed that little lip section into the strut top hat which caused the thicker part of the piston that you can see rest where it was supposed to under the top hat. Personally once that lip gets pushed into the strut top I don't see it ever being a problem as once the nut is tightened that top threaded and lip portion should not move through the strut top hat so no extra wear should occur.
So the noise you heard was deffinetly that little lip section going into the top hat. Then the larger diameter outer piston wall coming to a rest under the top hat like its supposed to.
Here is a picture that might help explain what I am talking about. Please excuse my MS Paint skills