Interesting. By reducing the width of my browser I find the point to be at 768 pixels.
So, if when you turn your iPad to landscape orientation, you probably get a different effect than turning it to portrait orientation. Does it?
And this situation also changes depending upon the size of the iPad that the user has. The "sliding" behavior is what I think most people would want when viewing moodle on their computer, so I don't think you want to always overlay, do you? And finding that sweat point, whether it is 768, 640, 100, 1024, will always still present the situation based upon all the varieties of screen sizes.
Hmmm, my suggestion is to not worry about the current setting.