Not necessarily - the main reason why I don't want to store my notes with Evernote is because I want to be able to use them in 50 years, not because I'm opposed to sync them with a 3rd party server.
for the AppStore version. (AppStore apps get their own mini-filesystem.)
You should be able to back this up and use it at any time in the future without Evernote. You do have to make sure you regularly sync and backup though.
Edit: I would like to add that I like the idea of using markdown, however. Evernote docs often contain undesired baggage from the original clipped html.