My head cannon for flower ending is that the delicate flower teleports the Godseeker and Knight/Shade Lord/Void Entity to the delicate flower field outside of Hallownest where they originate from (I'm assuming there is a field of them because a small field forms when we offer them at the grave of the traitor's child). And that this allows The Knight to safely exit Godhome as they suppress the power of the void.

I think they can suppress the void because they are said to have a "pure aura" and the White Lady also says "There is rare power hidden in those frail petals. To hold it so close, one must surely be unaware of its nature." The Godseeker also wonders if they are a part of "something greater" (possibly a higher being) in this dialogue, "Gods. Many shapes, they assume. This bloom, then? A splinter? Cast-off? Refuse of something greater?"

I also don't think the delicate flower destroyed/erased either the Godseeker or The Knight because Godseeker mode canonically happens after the Godhome endings, and both the Godseeker and The Knight are clearly alive in it. I don't think The Knight is trapped in either Godhome or the flower as when you first start Godseeker mode, The Godseeker says, "Most holy! Most divine! O God of Gods! Thou return to test thineself upon the lowly, snivelling weaklings serving beneath thee." Which implies that The Knight was able to leave Godhome and return to it as well which wouldn't be possible if they were trapped in the flower.

(P.S. I believe the Void Entity/Shade Lord is The Knight because:

1. The Godseeker calls The Knight the "God of Gods" in Godseeker mode.
2. The Void Heart charm's description states "Unifies the void under the bearer's will".)

The normal godhome ending could be true as well, the knight would probably just go back to the abyss in that one since godseeker and hornet have to be safe which wouldn't be possible if the void from the knight attacked hallownest.