The public understanding of the publisher/developer relationship is kind of fucked, to put it mildly. BEST CASE SCENARIO, they understand the focus of the game from the beginning and coordinate to keep it faithful to their initial goals for the project and the devs' as well.
SEE: Psychonauts. Ed Fries championed the project while he was at Microsoft, and unfortunately when he left, they were looking for games to cut, and Psychonauts got the axe. Double Fine had to hang on by their fingernails for a while until they could find a publisher who WOULDN'T want them to change just about everything "so the mainstream gets it." Thankfully Majesco picked them up, but had no idea what to do with it, so they released it to a blaze of no publicity at all. Not a great publisher-developer relationship, but on the plus side they didn't swoop in like "WE WANT RAZ TO BE ABLE TO KILL PEOPLE WITH LASER BRAIN POWERS NOW!" Double Fine obviously wasn't going to tolerate that shit, and their resolution on that very nearly put them out of business. Major props to Tim Schafer for many things, including sticking to his guns on that one.
If you're making something with a certain artistic bent that you're committed to and the person funding it runs in and demands that there be clowns involved, what can you do? You can attempt to put in that feature in a way that 1) somehow works and 2) satisfied the "money," but often you're not given that luxury - you don't have extra time or money to do it or you can't wedge it in with subtlety.
YES, art can work well within constraints. But often a money-based structure means that you have to make changes PURELY because of a business reason or some preference of a higher-up, irrespective of the needs and focus of the game itself. So I say YES, they can be art, but if you have someone screeching that a dreamlike, cerebral experience like, say - Ico - needs to have a bit with shooting or HAS to have titties in there somewhere, it becomes significantly goddamn harder to make it something good, let ALONE "artistic." That is my point.
Business and art aren't polar opposites. They just often don't coexist very well.