iOS Enterprise App not from AppStore – any warranty issues?
You can't void the warranty by using non-App Store apps.  The warranty covers the hardware of the device, not the OS.

Thousands, or hundreds-of-thousands, of corporate and school users develop and use apps that are not vetted through the Apple App store.  In fact, Apple encourages this type of activity.  Their own site for enterprise development states: 


  The Apple Developer Enterprise Program allows you to develop proprietary, in-house iOS, and watchOS apps that you can distribute to your users in your organization and outside the store.


What you're told by the Apple retail employee is completely wrong.