A show/movie/series is in the process of being financed and you have sales teams going around to Media Agencies and/or direct to brands (usually media agencies are the first contact) and they pitch the show with the available placements for product placement.
Cars, clothes, drinks, food, shampoo, you name it - everything that's on screen it's sold.
If it's not sold it's unbranded, even if you recognize the product by it's shape, the logo can't show.
So basically what happened so far is that the sales team approaches Apple Media Agency or Apple directly and pitch them the movies/shows and the characters with enough relevance/screen on time, and ask if they want to place their product with that character.
Probably it's even a guideline nowadays that the agency account manager doesn't even let villains, crooks, etc placements even reach Apple brand management because they know the brand guidelines to not be associated with "Evil Characters".
After some time they don't even pitch those placements to them because they know it's a direct "No".
If it's a yes then there's a series of meetings to show the script/story board where the product is actually placed and shown, and some brands even have a say over the directors in some shots.
In some sets there are usually brand representatives with the respective media agency contact.
No idea if it's like this on Hollywood, but should be something in these lines.
Trademark owners may object to the use of their trademarks in fictional films or other media productions without their consent, and seek to enjoin such uses by filing a trademark infringement action under section 43(a) of the Lanham Act (15 U.S.C. § 1125(a)), unfair competition in violation of the common law of New York, under the Federal Trademark Dilution Act ("FTDA"), and dilution of trademark in violation of New York's anti-dilution statute (section 368-d of the New York General Business Law).
The cited paragraph would be true of a movie like Harold and Kumar go to White Castle because the brand name is part of the title of the movie and the brand plays a major part of the story.
But it wouldn't apply to an incidental use of a branded product in a production, i.e., a car chase scene whether the brand of the car or vehicle-specific features are irrelevant.
I assume companies can say, no random director you cannot use a Microsoft Surface to nuke the world.
There must be something about it showcasing a product in a negative light.
But if you use a iPhone to hack the matrix and bring down the Italian government. Someone somewhere is going to assume iPhone is better at being "bad" than other phones. Regardless how true it is.
Apple is attempting to prevent their phone from being used to do bad stuff.