Is it permissible to buy from a website acting as an agent that displays goods for other sellers, where the seller sends the item to the website for packaging and dispatch to the buyer with cash on delivery, or is this considered the selling by the website of what it does not own?

There is no objection to dealing with a website that sells goods on behalf of their owners, as it acts as their agent. This does not fall under the religiously prohibited sale of what one does not own, because the hand of the agent is like the hand of his principal. There are other permissible forms of dealing if the website is not an agent, such as salam (advance payment) sales and brokerage.