The exceptions are: SMS, Settings, and the Phone app for the numbers tied to your SIMs (there’s still a billion VoIP options including extra lines from carriers like T-Mobile’s Digits) and probably a couple others I’m forgetting. I think the Clock app has a couple of privileges not available to 3rd parties actually.
You can use a 3rd party browser, but that browser will use the version of WebKit that comes with the operating system (except soon, in the EU, whenever 3rd party browsers with their own rendering engines ship there).
* no alternative browser engines
* no alternative wallet apps
* no alternative app stores (specifically so Apple can capture a % of sales)
* no software streaming
* no super apps
* Apple-only special SMS features
* Apple hardware (watches) get special access to iPhone hardware
that stuff adds up