I can't entirely recall if this is a big problem anymore, but I believe I have the solution of where Soul of Sectonia appears in relation to the storyline.
Ok, so let's start this off by saying The Arena and The True Arena are not canon. At all. Let's also say the ending of Kirby: Triple Deluxe isn't canon, either.
Keep your cool; let me explain.
Remember how the stalk Sectonia is on collapses after Kirby defeats her initially? And then he does his little dance, whatever. Shortly after, Sectonia grabs him with a vine, Dedede knocks Kirby unconscious and tosses him a Miracle Fruit, yadada...Right, well the canon differs here. Let's say that Sectonia was truly defeated. She collapsed, presumably dead. Kirby does his little dance, and presumably begins to head back to the Castle, where Dedede and the others are waiting.
Taranza's presumably in tears at this point, as it says that he and Sectonia used to be close friends, but let's ignore that point, for now.
He's almost there, when four Miracle Fruits hover down. Sectonia's vines, seemingly acting on their own, grab 'em, and in turn, Sectonia thanks them by devouring the four of them. And thus, bam! Soul of Sectonia. What I'm trying to say here is that the ending of the True Arena is actually the True Ending to the game. Consider the Story Mode ending a..."false ending" of sorts, like the "Bad Ending" to Kirby's Dream Land 3, and Kirby 64. If it doesn't quite make sense to you, let me explain further. We can all clearly see Sectonia falling over once Kirby beats her the first time. During the True Arena battle, it's clearly visible she's getting back up. Plus, she was completely obliterated with Kirby's Hyper Beam during Story Mode, making her existence completely impossible, meaning that the game does indeed show a split timeline. It was also morning, whereas her Soul fight was during the night, and transitioned into day. (In truth, the stage is stuck in a perpetual half day, half night cycle.)
Thus, this would mean that it is entirely possible Soul of Sectonia's boss battle is the True Ending to the story mode. While the Story Mode ending didn't play after her defeat for obvious reasons, her defeat is similar.
What do you think, if anything? Leave a comment below, telling me if you agree or disagree. Thanks for reading!