I have my object in blender that I UV mapped and baked. When I Apply the baked texture to that object in Unity it is not properly mapped. .BlendFile
The first UV map in the order will be the default. Since you baked down your materials to the joined01 map this is the one that should be default. The exported mesh should have joined01 as the first uv map and you should also add a light map uv (for baked light) as the second.
(As a side note: The exported mesh should only have relevant material slots so you should also clean up the other materials from this mesh. Otherwise that could potentially add render time to the final asset)
This question is more related to the game engine of choice and may be out of scope for this forum.
You have two UV-Maps on the object. The exporter might have either just exported the wrong one or exported both and you need to pick the correct one in Unity. Either way UVMap is the one you want, judging by the node setup, not Joined01.