In addition, Chrome extensions can't use JavaScript that is loaded from an external source (the review team enforce this).
This means that the code that enables Honey to hijack cookies and inject its own affiliate links must be in the Chrome extension's code i.e. the same code that the Chrome Web Store team have access to during the review process.
They wrap all their magic behind that single click, but to be fair, that's exactly how the traditional coupon code sites (e.g. retailmenot) have always worked. Honey just wrapped it into a browser extension and promoted the hell out of it.
The web store mainly serves as a payment gateway.