Looking through this on the memberlist config you can only identify alts by text in the notes, whereas in the wowroster default config it can identify by a rank. Is there a way to have memberlist use the rank(we have a alt rank to identify all alts) in the same way to identify the toon to the main? Or is this not possible? I'm guessing the data of what toons are tied to what account is not captured.

As you're saying yourself, the rank does not include information on what main an alt is tied to. This means the standard main/alt display of memberslist could not be used.

What exactly do you expect ML to do with the alt information?