I do miss the abilty to select areas of an image for Super Focus. I seem to recall that an early version had this option. Currently, applying Super Focus over an entire image will over blow clouds with greens and purples.
The process where the whole picture is processed has not changed from v1 to v2. That remains the same. The only difference is the v2 model’s Custom Selection is only available in after the render, that is a limitation of the AI Model. It does not “add” any process time, as the v2 model is much faster, and v2 still processed the whole image even if a custom selection was chosen. Once you have the process done in v2, then find the Edit Selection panel and select the areas you want!