I'm not sure exactly how to ask this question, but here goes.

Is there any functionality that you lose by not using the integrated email client (system notifications, unified/threaded messaging, etc)?

Actually my question can even be more generic when considering using third-party software for "core features" and then that software not implementing/utilizing platform specific "hooks" for certain events, settings, etc.

Here is a sample scenario, the new email sound notification. You specify which sound based on your profile (General vs Silent). But if you used third party software would/could you lose that functionality...so if you had another program that changed your profile automatically just because you were on "Silent" it wouldn't actually change the notification sound (since it wasn't aware that you actually received a new email). Again, this is just a sample scenario that may/may not be valid, but the general idea/concept is still the same.

bump...no thoughts or input?

All these things depend on the kind of integration the third party application has...

Probably you won't have any of the things you comment