Exactly where does it say that HTML, CSS, & Javascript has to be source code? If browser differences cause you so much grief, why don't you just treat whatever goes out to the client as "object code" of your own engine.
That engine would have to create a different page for each browser that you decided to support. Sure, it would be 4 times the work for every page, but that's work done by your engine, not you. Browser differences are accomodated through maintenance to your engine, not every page or library.
IE is not going away any time soon, so your output better be able to handle it's DOM. While you're at it, take a look at your user's resolution as well, and serve it the way they want to see it, not what you decided is best. No one likes horizontal scrolling or white space on the edges.