They still replace the referral code even when there's no coupon found, it's actually unrelated. They go through hoops to trick you into clicking useless modals right before checkout, and snag the referral reward using these clicks. This is what made people angry and uninstall the plugin.

The script they gave youtubers to read is also a bit of a lie, they don't apply the best coupon they're aware of if the merchant has paid what is essentially a ransom to forbid Honey to apply these coupons the merchant would like to keep more exclusive.