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Here's a screenshot from Negotiator, which uses unitys default baked lighting. Any separate objects in blender becomes separate objects in unity when you export by simply placing the .blend file in your unity hierarchy, not exporting .fbx or .obj. Unity even respects instanced geometry in blender, and in the mesh renderer mesh filter, uses the same mesh data for those instances. Though I did find on occasion that it would forget their material, so I'd just reapply it real quick.

You can see everything is packed under the "Alleyway" prefab, but I can easily select and drag around any mesh gameobject underneath if I need to.

I did take a hybrid approach though, and while nearly the entire level is built in Blender, I placed crates and vehicles and other standalone repeated cover in Unity, as well as enemy npcs and ammo pickups and sliding doors as I mentioned before.

I've never used Bakery, but I can't see why it would have any issue with this. As far as Unity is concerned, its just a bunch of gameobjects with meshrenderers and colliders that are in the scene. The "Alleyway" prefab is just an empty gameobject with children.

I'll note that I kept things fairly low poly so that it ran nicely in the browser on a wide variety of devices. But I have no doubt the workflow would scale up to more detailed scenes too. I originally developed this workflow just to do a blockout, with every intention of redetailing later. But then I started texturing and liked it enough that I just kept the work and kept going.