Version 2.8.2 is now available in the asset store.
This is a big upgrade with three new features.
1) MeshBaker now includes its own texture packer. You are no longer limited to packing textures into an atlas that is a power of two. The included texture packer will pack an atlas that is just big enough to hold your textures. The included texture packer also packs textures one at a time instead of holding them all in memory at once. This will hopefully eliminate MissingReferenceException problems.
2) ShowHide has been added to the API. This is a faster update. Vertex data is not altered in the mesh. Only the triangle array changes.
3) MeshBaker now tries to choose and configure the result material shader based on the objects to combine. This means that most of the time you won’t need to fiddle with the shader on the result material. This is a big workflow speedup particularly when using multiple materials.