Currently, opening a file in the Finder will open the file in the last-used window (if "open_files_in_new_window" is disabled, which imo it should be by default). However, this is not very intuitive as I won't necessarily want the file to end up in that window.
It would be handy if we could designate a "default" window that new files are opened in (perhaps clicking a little icon on the window somewhere).
The way BBEdit does it that I find works quite well is that new files (that aren't already open elsewhere) open in a single non-project window. Typically I will have a bunch of project windows open and another catch-all window for misc files I'm working on that don't belong to an open project.
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