I'm sending this in case you don't read my answer.
Someone asked Alicealeen about the relationship between Qingyi and Naruto on your behalf, to avoid an abrupt change in lore.
And yes, it's confirmed that the person Naruto searches for in each life is Qingyi. They existed before the Aeons and went through several lives, sometimes meeting and sometimes not.
Below is the answer I saw from Alicealeen, which addresses your question about the Otsutsuki.
The Otsutsuki are the gardeners of the imaginary tree and the Quanta Sea, their homeland. They created it, if I remember correctly, so in the fic's hierarchy, the Otsutsuki are above the Aeons.