We also grappled with this issue in the U.S. not long ago. While I’m unfamiliar with the administrative structure in Poland, if a city occupies a space at multiple nesting levels and there aren’t three different jurisdictions in reality, then I agree that there should only be a single boundary relation, not three. San Francisco is equivalent to both the neighboring level 6 counties and their level 8 cities, so we took the approach of only setting admin_level=* to the most relevant value (the numerical lowest), mainly because a semicolon-delimited value list is so rare these days, unlikely to be supported by any software, and overkill anyways.
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