Horizontal position differs from up-stem to down-stem notes when staff is scaled

I would disagree about calling this a bug. I call it a surprising feature for the situation. You have put the notes the same distance apart that you would have if both were in the same staff on spaces separated by a single line, but the top in voice 1 and bottom in voice 2 and increase the scale. For example, when the top note is C above middle C and the voice 2 note is the A below that, the notes start to offset as you increase the staff scaling.

First: you are right to have abandoned this approach in favor of changing the scaling globally in Layout / Page Settings. That way everything scales uniformly, including the distance between staves, elements not attached to one specific staff, etc.

That said, I do think you've uncovered a bug, and a kind of surprising one in that I'd have thought someone would have noticed this before. Upstem and downstem notes are treated differently in terms of where there "origin" is considered to be, and there are some specific calculations used to make sure they line up vertically by their noteheads and not their stems, that good things happen if the notes are of different widths (quarter note and whole note, for instance), etc. Apparently these calculations are taking the scaling into account incorrectly. This is true whether the notes are in different staves as in this case or different voices in the same staff.

I see the same result in builds of 3.0. Would you mind reporting this formally to the issue tracker (eg, via Help / Report Bug from within MuseScore)?