I think what you're talking about is just that: history. There is a slew of email, weather, web browsers etc. All in the App Store competing with their native versions. There have been for a while.

They also have a more recent history of literally promoting "competing" maps applications in the App Store after a botched launch of Apple Maps.

Google Voice for example. Apple felt that another app having a dialer would be confusing to users. I'm not sure what excuse they'd have to block Google Maps, given the large selection of mapping apps available, but I wouldn't put it past them to come up with something.

Google Voice is in the App Store these days. It's pretty clear that they've worked to come up with a fairer and more consistent set of approval guidelines.