I think you've hit on the correct phrasing of the question raised in TFS: Are people who use the extra features are going to get screwed? Depending on how you look at it, either yes, they are, or no, people who only want a bare-bones car are finally off the hook subsidizing stuff they don't use. There's two problems, one a universal economic one and one practical:
Economically, the seller is partitioning their market which allows them to capture more of the surplus by filling the area under the demand curve with a stair-step market price line rather than a level one. The bare-bones people will pay less, but not save as much as the feature-users pay out in increased prices. The teller will be if people can be hoodwinked as easily with monthly car charges as they are with cell phones and cable (being a rational economic actor can save you a ton of money!).
Practically, cars are not like software. Carrying extra pieces of car around costs a lot more than having extra code sitting on disk. With fuel economy a feature of ever-increasing importance, the seller who gains 2 mpg by not including disabled hardware has a decent shot at the sale.