They do this to not interrupt the purchase flow, not to be scummy. Opening a tab in the foreground or refreshing the page is extremely annoying to users and merchants request it to be in the background so it doesn't hurt their conversion.

I never said Honey doesn't override cookies. I'm not saying this isn't a problem, it's just not a Honey-specific problem. If the affiliate networks used first-click or multi-click attribution, none of this would be an issue.