Yes and you can find more about this in my other article: https://stackoverflow.com/a/14550417/1848600, search for: Methods of markup enhancement prevention.
To make it short:
It can do it by adding this attribute:
data-enhance="false"
to the header, content, footer container.
This also needs to be turned in the app loading phase:
$(document).one("mobileinit", function () {
$.mobile.ignoreContentEnabled=true;
});
Initialize it before jquery-mobile.js is initialized (look at the example below).
More about this can be found here:
http://jquerymobile.com/test/docs/pages/page-scripting.html
You also need to use data-role="none" on a content because if you use data-enhance="false" popup will lose its styling.
Word of advice, find another implementation of popup. Basically you are using a nucler weapon to kill a single fly.
Example: http://jsfiddle.net/Gajotres/PGL5t/