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Holy moly, this drives me crazy too! I would love for this to be resolved somehow. Either a separate shortcut for something like "Quick Add Next Matched" or just modify the behavior of Quick Add Next.

A very late follow-up: I noticed that this was implemented at some point—thanks so much, it's much more comfortable now!
This also happens when dragging a folder from the Finder to ST's dock icon: it opens a new window with that folder as a virtual "project" which is great, but the sidebar is collapsed. So my first action is ALWAYS to grab my mouse and expand the root node.

Interestingly, when opening a folder via the command line "subl ." the root node is expanded by default which is correct in my view.