if your code changes in such a way that it needs an updated table.tmpl, you have to remember to change all the template copies, and that sounds like a monumental pain in the ass if production code is affected.

That is exactly why I said that this technique is a demonstration of presentation logic seeping back into the application. It's why I argue for a more powerful template language.

Having per-project presentation tweaked solely by CSS is nice in theory, but doesn't cut it in practice. That does not mean you should mix presentational markup into your generated HTML; you should still generate semantic markup and use CSS to style it — the most immediately obvious benefit is that you won't need to touch your templates as often.