There may be more to this than we think.

When Microsoft updated Windows Phone 8 to 8.1 they decoupled a few system apps like Music and Xbox to make them easier to update.

This unfortunately resulted in them going from lightning quick to unusably slow. An enterprising developer even discovered the system music player was still locked away in the OS and sold an 'app' that unlocked it!

Apple might keep its native apps within the system because outside of it they may end up slow and terrible.