I'd say that the scene complexity is a bit too high for everything to be CG. Some of the lighting effects (on walls/floors for example) are very complex and too "real" for CG - basically, it'd take far too much effort. The bokeh (out of focus) effects are a bit too real too.
I'd say they took real photos and made them look like cell paintings. You sometimes see manga where they've done the same in backgrounds... maybe this is the first time for anime...?
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