So the primary goal of those shows are to sell the source material? The thing is, they always have stuff like external marketing that is anime specific (for cafes, for department stores, etc.), and then there are the absurd home release prices.
Then there are anime original shows. I guess it makes sense that the motivation behind making an adaptation like that would be to sell the manga volumes for an ongoing work, but I guess what I'm thinking about is that they are surely thinking about how much money the anime itself can make as well.
I don't know enough the business behind licensing and how profit is generated in the anime industry.
Anime for the last decade or so is generally produced by a production committee consisting of (roughly): the manga publisher, a publisher for the anime, one or more animation studios, vocal talent agencies, music publisher, various toy/goods manufacturers. Sometimes these are all individual companies, sometimes they're a megacorporation that owns multiple parts (e.g. Sony, who may be the publisher, own the animation studio, and have a particular musical act they want to promote). They all put various amounts of money into making the show in exchange for certain rights - home video rights, choosing the music and artist for the OP/ED, merchandising, etc. Nearly all the things like café tie-ins, department stores, etc. are just advertisement and merchandising for the anime, which in turn is advertising for the source material.
Shirobako goes into some of this. If you haven't seen it, I recommend checking it out on Crunchyroll. It's an anime about how anime is made.
ANN Answerman has also covered related topics a few times:
Being A Member of a Production Committee
Who Actually "Owns" An Anime?
Why Does Unfinished Manga Get Adapted To Anime?
Sorry it's sort of a tangent, but I figured some of you all might find it interesting given the question came up.