Yeah, I don't know about Apple at fault, maybe bluetooth but not USB.
I pulled the stock nav out right away in my truck with a Kenwood. Not matter what iPhone is plugged in or iOS version it keeps on playing. I have a Pioneer in my other vehicle also and never listen to AM/FM or CD, iPhone only.
Every once and a while I may have to unplug/reconnect to get it to recognize, but not very often.
USB is a somewhat standardized protocol for power and data transmission, but it's not entirely set in stone. Additionally Apple does not use USB, they use a Lightning standard that is translated to USB.
For example certain features on newer phones such as "quick charge" do not work when the non-specified USB cable is used (also I found this out recently when I was given a wireless charging pad for my phone that using anything other than the USB cable provided with the unit will have my phone not charge, even though the pad lights up). A lot of issues I have seen with connection issues via cable (mainly Apple, but not limited to them) have been crap quality cheapo cables because apparently people who get suckered into paying for Apple's enclosed tyranny of a system or buying another brand of phone can't afford quality cables.
Additionally ontop of charging commands issued through the USB cable, data processing is done on the headunit and iPhone side (and/or other brands). A breakdown in communication between either will result in issues, much like plugging in a "Plug & Play" item in USB that has either corrupted or out of date drivers on the hardware side, the computer might not even recognize the item being plugged in (though it might charge/be powered up depending on how it's made).
USB is not like an On/Off switch, it has various features and functions that are being expanded mainly through software manipulation; a USB system (cable, ports, software, hardware, ect) is actually communicating constantly. Hence my previous statement that Apple doesn't play well with others outside of it's iron-grip control on it's ecosystem and Toyota lags behind on using what information Apple provides through their datasheets for approved 3rd party users (though as far as I understand, while those sheets are very useful and informative, Apple doesn't really provide any support services though) to create regular updates. On top of that, updates aren't exactly beamed instantly to the head units, most of the time you have to get them done under warranty by going to a dealership (assuming it's being done under the warranty period, after that it's up in the air if the dealership is gonna charge you for it or not).
I see more issues with Apple products but it's not solely endemic to Apple itself, it's just how the infotainment system is designed and implemented. Toyota has decided they want to resist using Apple/Android hybrid units and continue maintaining their strict hold on what a headunit should be. So I would not expect this type of issue to go aware moving forward, sort of how they've decided to use Start/Stop tech in their engines now despite other brands using it and dropping it, and users being annoyed to hell by them.