I agree — it doesn’t seem like a problem easily solved. Indenting the first system of a flow won’t really help on a piece where the instrumentation constantly varies, and manually indenting each system seems very tedious, especially for a long score.
I looked at a number of published pieces to see how publishers handle this, and it looks like they usually put the labels inside the “music frame,” not in the margin, just like Dorico — but that they add extra padding on the left of some systems so that the left barlines still line up. I couldn’t find any examples where the left barlines were not aligned.
I’ve attached three examples, from three publishers. (They’re PDFs, so I had to put them in a zip file...)
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