Frankly, I don't see that much of a problem here. First of all, Amazon views Prime as the default experience and naturally shows that pricing more prominently.

Frankly, I don't see that much of a problem here. First of all, Amazon views Prime as the default experience and naturally shows that pricing more prominently. Furthermore I think it's naive to assume that pricing should be the key factor for their ranking. As mentioned, there are probably lots of details that influence the ranking, however as an anecdote I can say that shipping by Amazon and Prime-enabled is one my personal key requirements. I'll only use third party sellers if there are significant pricing differences or no other options. I wouldn't be surprised if other customers behave the same way, regardless of preferred ranking.