My good friend who applied and interviewed here also received a letter in the mail stating they were on the "alternate list". They also have several classes now listed in their portal that need to be taken before their application will be complete.
She called admissions and talked to someone there after receiving the letter and they were very nice. They flat out told her that those put on the alternate list had a strong enough application to get an interview invitation and had also done well in their interview (or would have gotten a rejection letter). But until her application was closer to being complete, they cannot offer her an acceptance. In the letter it pretty much explained this too, I guess, and stressed it was important to keep them updated on any changes regarding their application.
So, basically I do think they may keep them a bit separate (those told they are waitlisted....if you read through the thread, you'll notice some on this thread had to call them to be told they were on a waitlist). There can be many reasons why someone is waitlisted other than their application not being complete.
My advice would be to call admissions and ask some questions and find out the specific reason you are now on the alternate list. It very likely sounds like it's because you still have several prerequisites to take.
Good luck!! 🙂