This phone conversation seems like a jokey prod at Flowey’s existence, but tiny lines tend to mean things we don’t expect in this kind of game. So…
>We learn here that the flowers (which originally sprouted from the seeds stuck to Asriel in Asgore’s garden) spread all over the underground, seeming to have “a mind of their own.” We also generally theorize that Chara’s essence is with Frisk, right? Not their SOUL, since that’s long gone, but their essence. But if Chara’s SOUL broke in the garden with Asriel, how did their vague consciousness get all the way back to where Frisk fell?
>Theory: Asriel awoke with the determination in the first flower that sprouted… but Chara’s soul essence/dust spread further. It was across multiple flowers, and the flowers spread, sending Chara all around. When Frisk first fell onto a bed of golden flowers, Chara’s essence was part of those flowers. Finally having found a suitable human vessel, the dust/essence somehow got into Frisk, and that’s why you have Chara’s narration (at least in the merciless run?).
>Also, the second time you hit a bed of flowers (in the trash dump), maybe you get an extra dose of the essence, which is what triggers Frisk experiencing Chara’s memory while they’re unconscious.
tl;dr Chara’s essence is spread all over the underground by the spread of golden flowers (instead of all concentrated in one flower like Flowey) so when Frisk hit the bed of golden flowers, they got Chara’s dust/essence on them and Chara latched on to their determination. And that’s why Chara is supposedly the narrator, at least in merciless runs.