The changeling is native to wherever he was born (by definition). This is probably the material plane, unless something in your character's backstory says otherwise.
When planar bubble is cast on a githzerai, the bubble mimics Limbo because that's where the githzerai in question, like all other githzerai, was born.
Racial Emulation allows the changeling to count as another race for all purposes. Are you saying this shouldn't include where they are native to?
Where a person was born is a property of the individual person, not of that person's race or genetics. What if you use racial emulation to emulate a race with multiple homelands (such as humans, who typically live everywhere)?
From another direction: Why does
planar bubble make a bubble of Limbo when cast on a githzerai? If githzerai had a racial trait to make them count as native to Limbo, the changeling wouldn't get that trait (also, githzerai don't have such a trait). If
planar bubble said "When
planar bubble is cast on a githzerai, it creates a bubble of Limbo", then racial emulation would work - but it doesn't have specific language like that. Instead, the spell looks at the creature in question, asks "on what plane was this creature born?", and makes a bubble of that plane. If a particular githzerai happened to be born on the material plane, then casting
planar bubble on that githzerai would create a bubble of the material plane.