It doesnt seem to be possible. I see the
Bake Navmesh button in the editor calls this in the editor code:
Which by the name means it's not available in exported game, and probably not even exposed to editor scripting. It uses the
Recast library internally.
If you need that for your game, you have two options:
Either you generate your navmesh from geometry that you generated yourself already, and use
NavigationMesh functions to construct it: https://docs.godotengine.org/en/3.1/classes/class_navigationmesh.html?highlight=NavigationMesh#methods
(don't just take your meshes directly though, it's a navmesh so it needs to be offset).
If you need the editor baker, you could do a feature request on Github, or expose it yourself by modifying the engine (it's open source after all).