I baked out my normal, AO, and height maps from hi to low poly in Marmoset. Now I've' imported all my meshes into a single Substance Painter file using an FBX and I could apply each of the the individual AO maps to the AO map layer or I could just add them as an additional layer for the diffuse texture layer. Any reason to do one over the other?
The end point for this sculpt is Sketchfab, which also allows you to upload AO separate from the diffuse textures. Why do this? What's the difference really between just baking and merging your AO into your diffuse and keeping it separate?
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In game engines using AO as a standalone slot means that the AO can be shown only when those areas are in shadows — it wouldn't make sense to shine a torch at something and still have AO, so by keeping AO separate you can account for that. You'll have to decide if the extra texture is necessary on a case by case basis.