Baking in Blender does not support modifiers
I think it should. This is one really bad problem in Blender. If you want to create assets for example for games and you want to bake the pointiness value, you need to have Subsurf modifier. But you definitely don't want it in your final model, at least not applied one. That causes you to first save your object, then apply the modifier, bake it and then save the bake result and load the old model. This workflow works, but it definitely feels wrong to do it like that.
So, maybe the bake would during the rendering time apply all the modifiers and then undo that? Or something like that.
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