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Well, if there's a reason why the confusing part is desirable, I haven't figured out what it is, yet. About the only time I ever use it is when verifying my answers to questions about the stalled context :-)

Send in a query to the support ninjas and ask them why it works the way it does. My suspicion is that it was put in for symmetry and doesn't really get much use (or is used by people who only use it on leaf contexts). If the nesting behavior bothers you, but you want to use the stalled context filter, I think you could make yourself a perspective that simply selects nothing but the leaf contexts. Grouping by project, showing remaining actions, any status, with the column display enabled would give you a view that would let you quickly spot projects hung up because of stalled contexts. Or group by context if you want to go directly to seeing which contexts are stalled. Group by added if you want to see what has been moldering longest.

If you do end up making some lasting use of the stalled context filter, I'd be interested in hearing about it...