I would say “no problem” until I read:
These applications will be downloaded and installed by the employees of each of our customers.
It seems that your creation (set) of private applications that are intended for use only by specific users, that is, employees of the company.
Apple has a separate enterprise development program focused on this, which allows developers to deploy programs for their own company and do it outside the App Store.
If your program is very company specific, Apple may force you to do this - instead of putting apps for general consumption in the app store.
See here for more details:
http://developer.apple.com/programs/ios/enterprise/
also:
If your application is really intended for a wider audience, and in fact you can sell / distribute it in this way - you could "drop" the application dynamically. For example, at the first launch, when you “register” with some “service” - based on your email address, it can download the corresponding skin graphics.
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