I have done this scenario several times on multiple characters and I have never been given the option to skip this and I do no understand why.
Edit
Logging in and out doesn’t work and clearing cache/wtf folder did not help either.
Perhaps my account is not logging the completion?
I had to do it on a 2nd toon the other day. I couldn’t find a way to by pass it. Wished I could have.
Once you get to the halls of origination, for the first quest, you turn in with Magni and he gives you a new one, which sends you into the instance. As soon as you get that quest, telling you to go inside, talk to Magni and you should be able to skip. You still have to fly there though.