This doesn't mean that tablet form factors won't have the "desktop", I'm sure they will. And if so they can run the IE10 with battery draining Flash anyways. I don't see the point in limiting the IE 10 Metro.
They'll have the desktop, but people probably won't want to use it. It's a very clear statement that, going forward, plugins are being deprecated in IE. Creating content that doesn't require plugins is ultimately better for the web and applications too complex to be easily developed in HTML are probably better off as native WinRT apps anyway.