When MC dropped the glowing flower and a sea of them appeared outside, I thought it was the trigger for her disappearance somehow.The only real hook I see to Summer showing up in the present day is how Nami says "Summer's disappearance" at one point. That phrasing can mean that no one knows what happened to her. Leaving the door open to her reappearance. I dunno.
However, we now know that Summer did not vanish at the cabin but sometime later. Plus, this game seems otherwise to be pretty grounded without any mystical elements, so I'm still wondering what the deal is with those flowers.