Question: An application is closed, with customizations for certain companies, where it should not be downloaded by people without a contract. I would like information if it is possible that users download the same is not the Apple Store or Play.

Or it would create a specific version for each client in official stores. (Apple Store or Play)

Answer: 
<http://www.apple.com/iphone/business/apps/in-house/>
On Android, you are welcome to distribute your apps outside of the Play Store by your own means. You will be responsible for distributing updates as well, and your users will need to check the "Unknown Sources" checkbox in Settings to allow for non-Play Store installs.

I cannot speak for iOS.