This will be a boon to sites who have lost a lot of their revenue from their "custom search" function on their own website. As described in the article, Google has been squeezing these sites in order to keep more of the advertising revenue for themselves. (You can see it in their results by looking at how the ratio of money made on Google sites versus third party sites has been consistently shifting into the Google side of the pie)
Now I wonder if the EU will take on search engine front ends like startpage.com or duckduckgo who use Google results. Will they be allowed to run their own ad network alongside the Google results? If so that would make them a lot more viable.
Nothing will happen to those other sites because for this particular case Google has already changed its practice after the EU filed an objection in 2016. This fine is retroactive to cover the damages made during the 10 years of investigation. https://www.marketwatch.com/story/the-latest-eu-fine-on-alph...
Understand that there are two "kinds" of custom search. One, which is discussed in the BBC article is "AdSense for Search" which is and advertising program you could engage when you put a Google search box on your web site.
The other kind, which is not discussed here, is where you have a web front end like startpage.com or duckduckgo.com which is making an API call to a search index in response to your query. In the US, the two english language indexes with decent precision and recall are provided by Google and Bing[1]. One of Google's big partners there is Infospace which uses Google results in many of their properties. That said, when you use Google results in your search "engine" web page, you are bound by a different contract than the AdSense contract. And, like the AdSense contract, it is (or at least was) pretty restrictive on what sort of advertising you could do around Google's results.
[1] Bing either directly or through Yahoo!'s BOSS API if that is still a thing.
Now I wonder if the EU will take on search engine front ends like startpage.com or duckduckgo who use Google results. Will they be allowed to run their own ad network alongside the Google results? If so that would make them a lot more viable.