Separate screen of search results is just another tab in your browser - that's actually a vote in favor of web based gmail.
To make my example explicit above, suppose I have a "directory" structure with dirs like `conf`, `conf/iaq2016`, and `conf/gmu2012`. Then a search in `conf` will not turn up results in `conf/iaq2016` or `conf/gmu2012`.
Believe me, I check this once every few months, always hoping that google will have improved their "tag" implementation.
I do appreciate your tip about multiple browser windows, though. In general, I don't like having multiple windows open to the same application-- but that's my problem, and not a design flaw in Gmail's search.