i don’t disagree with your idea – in a world with unlimited resources. but i just don’t see a situation where there’s going to be a single de facto / preferred repository for GIS data any time soon, and in the absence of that, i’m guessing the cost / benefit balance for developing and supporting an interface to get data from Wikidata into iNaturalist and then back to Wikidata weighs much more heavily on the costs side.
take Goukamma Nature Reserve, your first example of potential duplicates in iNaturalist. it’s neat that there’s a way in Wikidata to find potential duplicates in iNaturalist, but you might be able to do something similar in iNaturalist. and if you look in Wikidata, there is not a geoJSON for that reserve. so Wikidata couldn’t serve as a source for geography in that case.
if you just wanted to add iNaturalst Place ID records to Wikidata en masse, i think that might be something that anyone with some coding skills could do…