For me, it was a matter of having the rubber flange on the wrong side of the bracket (strut). I thought I could have it on the top side, and still be able to draw it down tight. When I did, it pulled the whole thing right through the hole.
Discarded that well nut, grabbed a new one, put it so that the flange was directly on top of the roof, with the strut channel on top of that, added washers, inserted the bolt, and snugged it down. Adding to the level of 'fun' was that I'd already put a bunch of Dicor around the flange / under the strut, so it was pretty messy the second time around. Took some doin' to get everything cleaned up.
That said, there's a point where the bolt head draws down flush, and then where it begins to snug up... which is usually the sign to *STOP TIGHTENING*. There really isn't a hard 'stop' feeling like with a metal-on-metal fastener... so I guess if you just kept turning and turning waiting for it to get tight and stop, yeah, you'd pull the threaded insert right out.