The fee could be less and have a similar deterrent on the type of activity you describe. The real question isn't what Apple is gaining from this fee, but what they are losing.
Apple's $99 fee is annoying and feels like a waste of time and one more thing to manage.
The paid ADC program has kept me from sharing projects with other developers who would have otherwise been able to contribute (but they aren't paid devs because they'd rather have a year of Costco hotdogs than pay Apple to help me with my app for a week)
Apple should long ago make the $99 an App Store fee, not tied to any provisioning certificates or code signing.