Wikipedia says that total cost of ownership is: "a financial estimate whose purpose is to help consumers and enterprise managers determine direct and indirect costs of a product or system." The key point of this definition is "indirect costs;" it's the whole reason that this definition exists. To illustrate, imagine that you're sitting on your couch eating cheesy puffs and a commercial comes on for a slick looking sedan.
The driver is rolling slowly down a catwalk lined with underwear models who are leaning into the window and whispering, "we want you." You think to yourself, "That could be me!" You go to the dealership and the sticker price is workable if you trade in your old clunker, so you go ahead and buy it. Now you just need to keep an eye out for underwear models. Two years later, you haven't hit 60,000 miles and the sedan is falling apart. Every couple months you have to fix something and it's always expensive, never mind the headaches it causes getting it to the shop and car pooling to work with your grumpy sister-in-law.
Total cost of ownership in this case is the sizable hidden cost you pay replacing poorly manufactured parts and, nearly as important, it's the headaches you have to go through of dealing with these problems over and over.
I see this total cost of ownership issue occur regularly with clients who have had custom solutions built in Joomla (e.g. a custom component or general customization.) The culprit is often them making their initial decision based upon the direct cost, the Joomla developer's quote. The reason why is development is invisible. You can look at a design and see whether it's attractive. You can look at SEO rankings to see whether SEO is effective. But development is largely intangible for most people: so if it works, it works, right? And if development is a commodity, why not purchase on price?
Much like their real world counterparts, poorly engineered solutions cause problems. The same way a poorly engineered bridge can collapse, poorly engineered code will:
These are all indirect costs which can be compounded by damaging your brand in your visitor's eyes, leaking sensitive data, hampering online marketing efforts, and generally destroying your trust in your own website (plus the personal cost to you as you try and deal with this.)
The take away is that if you care enough to invest in a solution, your interest in a Joomla developer or development company shouldn't use their sticker price as the primary decision point. Take into account their experience, specialized knowledge, and track record. Exercise care making your decision, because they will be working on the foundation of your online presence.