My take on this whole situation is pretty simple: I don't think Phantom Seer necessarily deserves high ToC ranks. We don't have any information about surveys (except for, well, the ToC itself). I also don't think it's being put at the bottom purely because of bias or incompetence. There's so many possible reasons that we don't know, and it's simpler to assume there is one.
However, there is one thing that it's hard to justify: the lack of Color Pages. Why doesn't it get color pages for reprints, volume release or whatever?. You can imagine some excuses (it's unneeded because the series is growing regardless? The artist just doesn't want to do them?), but they are way less solid. They are an easy way to promote series, and even if surveys are terrible (which, again, could easily be the case), there are other metrics, ones we do know about for sure (such as volume sales and reprints), that should be enough to justify it. I don't think people would be that annoyed by the bottom placements if they felt like Jump was doing something with the series. But they aren't.