The second reason is that the physical USB-C connector is thicker than the Lightning connector. Not by much, but it really is; in fact, it's about as thick as...a 3.5mm headphone jack. Right then. (This is also why the wildcard option of putting both a Lightning connector and a USB connector on the phone was a non-starter.)
I know there's an argument to be made that it's all about the Benjamins, that Apple just wants licensing money and maybe to wave around the DRM boogeyman. Maybe, but I honestly think that's more of a happy bonus for them than an overriding consideration. They're control freaks who don't like to share with others, but they're regularly on board with non-proprietary standards when they think that's what makes a better product. Remember, they were one of the first major companies out of the gate with a USB-C (only!) computer, and Apple was involved with the design of the USB-C connector.