Supposing the following scenario: Company A asks company B to produce an IPad App for them. Company A only wants to use it for themselves on a very limited amount of IPads (
Company A can participate in the enterprise developer program and install proprietary apps on any of their devices freely:
https://developer.apple.com/programs/ios/enterprise/
Note: I've worked on several proprietary apps that we simply released through the app store at a price that would prevent others from purchasing it. It's the easiest way for the client's employees to get the app on their device and it has resulted in new business for us when others have seen what we've done.
Enterprise distribution is exactly what you want in this situation.