My experience is that the original waitlist does indeed count, and in fact overrides the airport standby time stamp even though both are required. I have even watched a gold who was waitlisted on a lower fare upgrade ahead of me a platinum paying full Y fare when the waitlist was already closed, even though I beat him through the activation at the airport.

I've also had it explained that the connection is considered "activated" when there is less than 4 hours between check-in for the originating flight and the connection. So if you're flying across country, you'd almost always need to reactivate when you hit the connecting airport.

But this doesn't penalize you--see above--since the controlling time stamp is the waitlist added time stamp.

Arcane rules abound but I'm determined to figure them out someday soon.