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EXACTLY! The SE's always expect sites to have links, always. However, they have become skilled at recognizing when the purpose of a sites links are to "juice" them up in the SE rankings. The more sophisticated the SE's become with "reading the tea leaves" the more affiliate MFA (Made for Ads) sites suffer in the rankings. One can see this by making some comparisons. If you were to look at a typical MFA site and it's performance in the SE's and compare the site and data to the new model in a site like the New York Times Wirecutter site you will notice that the Wirecutter rankings along with the other performance results are far superior. This is due to the Wirecutter content (including all its affiliate links) are riding on the back of a true content site, the New York Times.

Build a true content site with pure function and make a subset (separate area) of that site the affiliate linking content and offerings section. This works, I've been doing this with my content sites for quite a few years now. The SE's don't care about my affiliate linking area because their true interest is on my content, its niche popularity, the frequency of updating content, etc., etc.

You pay five, ten dollars, maybe a little more to go see a movie and they lose money on the ticket sale, but they clean up on that popcorn, nachos with cheese, the giant soda that is half ice, and the candy bar.