Take the tar command (please!), which is already a nightmare where lower-case `a' means "check first" and upper-case `A' means "delete all my disk files without asking" (or something like that --- I may not have the details exactly right). In some versions of tar these meanings are reversed. This is a virtue?
There's no reason they couldn't do both, really. They could have spaces for traditional ads, and they could have those direct partnerships.
Direct partnerships might be nice in theory, but it will always require a separate decision and process from the company to partner with Reddit. Considering there are hundreds of different avenues people could be advertising on, I'm guessing Reddit is kind of low on the list.