We had to pay $299 for the enterprise license to distribute iOS applications internally to just our staff[1]. This circumvented the App Store entirely and we used MDM tools (AirWatch) to distribute. Was this avoidable? I'm genuinely curious as I am not specifically an iOS/Mac dev.
No. In order to publish (even just within your organization) you need to establish a trusted relationship, and Apple charges for that. There is plenty of room for argument about how much Apple should be charging for this, but the process does have some costs to Apple, so it is only right that they charge something.
[1] https://developer.apple.com/programs/enterprise/