I agree, these are interesting questions. You propose some interesting analogies and the conclusions of them are hard to argue with. There is, however, a subtle point that gets lost in these analogies; Apple is the only publisher or merchant. Would your conclusions hold weight if a publisher refused to publish books with advertisements in them and they were the only entity that could publish books? Or what if they refused to sell clothing with advertising on it while being the only seller of clothing? I believe that in either of these cases the answer is no, if one publisher had a monopoly on the ability to publish books or one clothing store had a monopoly on selling clothes, that it would be unreasonable for them to regulate what books can be published or what clothing can be sold based on their own arbitrary opinions.
Unfortunately the waters are murkier than this. Apple has a monopoly on publishing apps for the iP* platform (iPhone, iPod, iPad), but other companies make similar platforms. Is it ok for one company to have a monopoly on (and use it to restrict) publishing for a particular platform when other competing platforms are available? After all, one could buy an Android phone instead of an iPhone and thus avoid Apple's restrictions. Is that good enough or does the market for each individual platform need to be free? I'm not sure how this might map into your above examples. The closest I can come is one merchant having a monopoly on cotton shirts while wool and polyester shirts are available from others, but that fails to capture the way you choose one platform and are locked into it for two years.