Some examples:
Only Messages and Mail can provide OTPs, again only when using the system keyboard.
When swiping the lock screen to the left, only the system Camera is allowed to appear.
When using navigation, only Apple Maps is allowed to provide the navigation overlay on the lock screen and Apple Watch.
After years, the default Mail app can be changed, but AFAICT that doesn’t do anything other than override mailto links. However, this functionality isn’t available for Calendar for example.
Similarly, you can’t override natural language Siri incantations to use your preferred apps. Like “message X” always uses Messages or “remind me of X” can only use Reminders. And alarms and timers can only use the Clock app.
I really want Apple to fix all of this, but I guess it’s easier to act like the “deletion” of system apps provides a level playing field. The real problem is that the default apps lack a lot of other features that only third parties provide - but Apple can’t be assed to improve them.