However, the rest (your conlusion) seems a bit too loose a standart to me. I think burden of proof should be on the side making such affirmative claims (that, this sample belongs to this species etc.).

I generally agree, especially with the part that 'species names and definitions should ideally correspond to the ancestral demographic structure of the organisms involved'. In fact, we started to learn a good deal about such processes thanks to recent genetic studies (thanks to yours as well) ...

isn't it part of a general problem though? doesn't this study (www.biorxiv.org/content/10.1...), for example, call into question ubiquitous species-naming in hominin taxonomy? also, doesn't it have any reflections in adaptive story telling?

This has some reflections on the neutral vs adaptive evolution centered debate too, no?