Kirk Biglione give some examples and he makes some valid points, such as why Microsoft doesn't use valid HTML including DOCTYPEs on their site (I've often wondered the same thing myself). But seriously, calling a font tag an “atrocity“? A little over the top, don't you think?
When you run the FrontPage 2003 Accessibility Checker on a page that has include pages in it, the Accessibility Checker doesn't check the contents of the included page(s). I'd recommend checking and fixing your included pages first.