Harmony patches with Carbon are redundant and can pose issues with users using carbon in parallel with random harmony patches. The assumption is that users doing this would understand the risk, but that's unrealistic. Most people wouldn't understand, nor would they care.
Carbon is built on Harmony and offers easy implementation of custom hooks without needing Harmony patches. If you're using Carbon, you don't need these patches. If there's a particular patch you want to use on Carbon, ask the developer to either ship it as a plugin or utilize Carbon's built-in custom hook feature to implement the desired hooks.
Harmony is useless without a framework. That's where Carbon comes in. Carbon is an upgrade over Harmony, so using both is pretty redundant. This isn't a matter of "restricting freedoms" but ensuring users cannot poorly implement it into our framework.
I hope this clears things up!