I think the biggest issue is that Rowling depicts the wizarding world and the proragonists as more or less unambiguously good, while brushing off a lot of the actually problematic things with it. They're literally the saviours of the universe and are never seriously questioned in-universe to the point of being labeled as a Mary Sue by many critics, so from that perspective it does tend to give the impression that she endorses all the aspects of it based on the fact that she frames all of it in an extremely positive light, whether or not she actually thinks that to be the case. She even explicitly wrote a passage in to shut down notions of elf slavery being bad in the story itself, which suggests intent in her depictions. In universes like 40k, the factions being depicted are quite a bit more morally grey, and the story actively goes into and confronts the problematic parts. She could have taken a more balanced approach and depicted the wizarding world as still having a lot of problems, and actually delved into the ethical and social implications of the various aspects of her worldbuilding, but she didn't. Even just depicting a small part of the wizarding world being against elf slaves instead of the one person speaking out for them and getting ostracised would have at least been a lot better from story and worldbuilding perspective IMO.