Hi, Eric. That's an intentional change from the most recent few builds which add quite a bit of dependency-based functionality to unit testing and code coverage analysis:
Context configurations are created based on a contextual selection, so they were never intended to be editable from the get-go. In fact, I had a big TODO about the checkbox tree still being editable for those, but while working on these new features, I figured out how to do what I originally wanted and make them read-only.
If you want an editable Apex unit test run configuration, you can -- as you noted -- create one explicitly, and you can change its selections as you'd like. Context configurations, though, are read-only based on the original contextual selection.
Regards,
Scott Wells