How do kepler orbits account for planetary migration?
Kepler orbits apply only to 2-body systems.

They apply only, if the masses aren't too large and the orbits aren't too close. Otherwise relativistic effects occur, as for the Sun - Mercury system.

Kepler orbits only apply, if the bodies are sufficiently spherical.

As soon as a third body comes into play, the system can become chaotic.

Too many conditions, especially for our early solar system.

Strange orbits like those around Lagrangian points, or horseshoe orbits can occur. Orbital resonance can stabilize as well as destablize orbits.