With an iPhone, unless you do other sketchy things to your phone to 'jailbreak' it, the only way you can download apps is through the Apple App Store.
Companies couldn't offer apps on a CD even if they wanted to.
Well at least with an android phone (I've never had the desire to own an apple product (not that I'm fond of anything google has anything to do with either) it is quite easy to 'sideload' an APK. You can even do it on an Amazon Kindle, without 'rooting' them.
And I HAVE purchased a few devices that did come with a mini-cd with their device's android app on it, although such is a rarity.
If I had an item that did not allow me to do anything with it other than what I buy from their company, I'd re-think my choice of supplier....
Kind of like farmers are now starting to re-think John Deere farm machinery because the manufacturer won't let the farmers service and repair their machinery themselves.