Yes, this changeset comment is not the best way to discuss the tagging.
It seems that the wiki has also no established solution for such nested POI. The other way round exists as well. You paid already a basic fee, but you have to pay extra for something. The later case is correct with a fee=yes, but can't be distinguished with this case here where the museum is included in the park entrance fee. Maybe asking in the forum to get some sort of common agreement on a tagging.