As you hint at, I think that the path forward is semantics. It would be great to have a way to mark that something is an ad, and something is an offer. Then we could establish reader mode best practices for those.
My assumption is that they wouldn't be invasive: ads with zero animation, just inserted, and offers included without overlaying atop anything. There are ways to make this work without breaking it.
I would also love if we could target it with media queries with a very minimal set of properties, perhaps no positioning or colour, but at least fonts and typesetting. Indicate a logo to use. Keep some soul to it.