Apply navmesh overrides from additive scenes, only ignore overrides from system scenes.
For some reason our startup scenes load as additive, so the navmesh settings of the startup scene would have been ignored.
Partially reverts https://github.com/Facepunch/sbox/pull/3555
We could also fully revert it if we want system scenes to be able to override navmesh settings.
3be8514e6d
