Thank you for sharing your finding with Unity.
ProBuilder workflows have known limitations with prefab instances in terms of stability and performance as well. I would recommend to only use prefabs with ProBuilder meshes when you won't have to modify these anymore.
For your case, the sphere modification, the important thing that impacts the most the performance is the number of subdivisions on the sphere. With 3 or more, it's gonna take a long time for any change done to the prefab instance (more than 1 min for a subdiv count of 3...). It's mostly visible here as this sphere has a large number of vertices (~4000) and all the overrides of the PB mesh are compared to the prefab one which is the operation that consume the most time. I would maybe advice you to Unpack your asset from the prefab when you want to modify it, and make a new prefab (or replace your previous one) when you finish your edit.
I'm sorry this is not an ideal solution, but as I said, this is a known limitation or ProBuilder with prefab workflows :(
We reviewed your report and determined that it's a feature request rather than a bug. We've logged this request in our system so it can be evaluated for future roadmap planning.
We will close this case as a feature request. While we can't guarantee timelines, your feedback is important and helps us prioritize enhancements. If you have additional context or use cases, please share them.