fundamentally, the issue is that the Location box tries to do too much. it tries to get an iNat place and fall back to a Google Place if no iNat place is found, but it tries to get an iNat place by showing you a list of Google places and matching your selection back to an iNat place. that matching is meant to be a convenience, i think, but as there are more iNat places created, the matching just becomes more and more problematic. there’s just not any matching algorithm that will reliably match (or not match) as a human would 100% of the time, even if you take into account the underlying geometries.
the only way to reliably resolve the matching issue (and other related issues) is to eliminate the matching process altogether. this means either (1) dropping the ability to filter by Google places altogether (as is done in the Identify screen and in the Android app), or (2) changing the Location input box (and the related More Filters > Places input box) to force the user to explicitly specify whether they want to select and filter on either an iNat place or a Google place.
there’s been talk of revamping the Explore web page for years, and one of the choices i outlined above should be implemented as part of such a revamp, but until that revamp happens, i wouldn’t expect this to be addressed.