Reposting the same comment I made on another post:
It's not just Honey swapping the affiliate codes. Practically all the major coupon sites do it too. That's why they require you to click on a coupon code to reveal it. When you click, they usually reveal the coupon code in a new tab, and helpfully redirect the current tab to the store, using their affiliate link.
It's more obvious when websites do it though, since they can't auto-close the tab like Honey does. They also don't automatically pop up at checkout like Honey does.
I imagine some of the other coupon extensions do the exact same thing as Honey though.