Doesn’t signify anything. Could mean that the person sending the request for the Skype interview did not see the waiver and was just lining you up for that requirement. Could mean the interview was first waived because they felt your paper app was strong enough without it but, when they started looking at the rest of the competition, decided they needed to talk to you in person to get another view of you against the applicant pool. See how you can make up almost any scenario?
Also, after the interview, do not try to read the tea leaves even if they gush over how well you did and how they can see you on their campus and how well you would fit into their community, etc. If you dig a bit here, you will find examples of interviewers who said these things (even ADs) and ended up with rejections as well as those who thought they completely blew the interview but were accepted.
Just enjoy the conversation. It doesn’t matter what you talk about, the school is trying to get a better sense of “you.”