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I really think that in the most recent case which is Aku no Hana, it's completely intentional. The premise is supposed to be. . . well revolting and the animation just amplified that even further (and they haven't even done anything yet).
If you guys have watched the disney short Paperman, that tries to combine the feel of 2d (for that more earthly feel) and 3d. There are many anime too that incorporate CGI in backgrounds (HSI, Hyouka, Ufotable films) and as time passes by, the animators get more techniques in trying to blend CGI and 2d together to the point that it looks pleasant to the eyes.
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