How to restrict an iOS app to iPad Pro only?
Within Xcode you can specify that an app is iPad only under the "Deployment Info" section of the target's General settings.

Beyond that the way to limit an app to certain devices is by specifying features in the Info.plist under the UIRequiredDeviceCapabilities key. You can see the options listed on Apple's developer website here: iOS Device Compatibility Reference

Unfortunately there does not seem to be an option that limits an app to iPad Pro devices only. You can specify "arm64" which will limit your app to iPad mini second generation and above, iPad Airs and iPad Pro devices. But I can't see an option that says devices that support Apple Pencil only.