I'd agree that some of the causes are unsolvable if you want a design completely unconstrained by the performance limits of HTML rendering environments. This is why some people build HTML apps that look like some native app they had and say, "this is too slow!" However, there are some very bad anti-patterns that cause unnecessary reflows, and those can be avoided if you understand them.

For example, many infinite-scroll pages add a small amount of content to the DOM and then ask, "Did I fill the page enough?" by asking for the new height of the page. Each time they do that it requires a reflow where the browser recalculates the height of the page. When the added content is small it may take four or five trips through this loop to feed enough content into the page. A better alternative performance-wise would be to make each chunk of added content a fixed height. That way it's easy to do the math inside your own code, add four or five chunks, and the browser will do a single reflow at the end.

If you look at the "flat" designs that are becoming common in operating systems and apps, they perform well in these situations because they are very regular and easy to compute. Things like rounded corners, transparency, and drop shadows all make pages slower to render.