Host same application with different design My question is similar to one posted in here but not exactly the same : Creating the same, double applications for iOS permitted?

We are building iOS application for museums, the idea is to create application(s), brand  it per museum by changing color, logo etc, update museum content and host it on app store.

All hosted application will contain similar functionality, but with different content, different users and different branding.

According to Apple review guidelines


  2.11 Apps that duplicate Apps already in the App Store may be rejected, particularly if there are many of them, such as fart, burp,
  flashlight, and Kama Sutra Apps


Does our application comes under the scanner of Apple because of similar functionalities between all of our hosted apps?
Only if there are already tons of apps that will let you navigate, say, The Smithsonian Museum of Natural History."  Then that one app for the smithsonian MAY be rejected.

But, I suspect there are not, so you should be fine.

Similarly, since you'll presumably be adding additional apps with different functionality, say the next one is for the Guggenheim, you should be fine.  The 2 apps couldn't possibly be used as a replacement for each other.

Apple's concern here is keeping out over-served functionality.  There are so many "fart" apps that yet-another-one can't possibly help any user anywhere beyond what's already available.  Museum apps are well outside of that scope, assuming you create a quality app with a great UI for museums that don't already have several hundred apps.