Unless I'm misunderstanding, the technology described in the article is designed to fight against cross-site tracking (i.e. following users all over the internet to different sites)
I suspect few users would object to a single web property remembering them across multiple visits.
So you'll have to rely on the webshop to keep track of purchases? I'd rather have a third party involved that has to keep both the publisher and the advertiser happy.
Maybe don't pay for clicks, only pay for sales.