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gbj_tester
I think coaxial is the right term. Non coaxial objects don't share a common axis, so if the BB cups are not coaxial then an imaginary line drawn down the axis around which the drive-side bearing spins would not be the same line around which the non-drive side bearing spins. This means that when you force the axle through them, one or both of them will be receiving a twisting load (in addition to the expected load). In a square-taper BB the bearings are held coaxially by the BB shell, but with independent BB cups they could be not coaxial.
I think the concern was that even if the BB shell had been faced then the introduction of the bracket between the drive-side cup and the frame could misalign the cups, since the bracket is not very finely engineered and is subject to other loads from the chain guard that it's attached to.