I usually set up my collections to use MultiMarkdown, in order to be compatible with other text editors I use or have used (iA Writer, Marked or messing around with PHP integration).
But I find I’m using these less and less as time goes by.
Is there any advantage to the Notenik format if I went back to it?
It’s possible that use of the Notenik format might be more reliable, since that’s the native format (and the one I use most often, so the one I’ve done the most personal testing with). But there’s no intentional hobbling of the other formats – other than what might be built into the other formats themselves. That is, some of the more obscure and complex Notenik field types might not really play well with a MultiMarkdown format, for example.