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I know what you mean about having some in front and some in the loop. V3 is, to me, definitely better in the phase department, but there's some subtle distortion being added by having it in front. I've got a Boss Super Phaser, among others, so I know what you mean.
With the reduced low-end when engaged, I believe ET did that on purpose (I forget the reason why at the moment, though). Actually, I think it emphasizes the high-end, which is perceived as a low-end loss. If you set the MF to DSP bypass and not true bypass, it's much more consistent between bypass and active, which might help you offset it with your amp.