The Pluto system is anything but stable. It’s an extremely chaotic system.
Pluto could be a former moon of Neptune... or it could be a Kuiper Belt object perturbed from a more distant orbit... or it could be a captured interstellar object. There are many many possibilities other than “as it is now, so it always was”. Planetary formation theories are extremely raw, wild guesses, and new data constantly forces changes to them rather than confirming existing hypotheses.
Thing is, NO sane informed theory involves Pluto springing into existence and achieving a tranquil orbit in just 100 human lifespans.