Besides the forums, I also looked through the Engraving and Notation Options, specifically searched through the different voice options. I found one that should prioritize the higher notes to the left, but in practice when I have three voices it changes the rules and I can’t figure out why.
What I have done so far is move the middle voice to the right via the Engrave option so that the bass and melody align, but there must be a better way than that.
I’m not sure which option you’re referring to, but you could try in Engrave mode explicitly setting the voice column index for the lower notes to 1 and the upper notes to 0.
You can do this after you’re done entering notes by selecting all in Write mode and filtering by voice, then switching to Engrave mode; your selection will be preserved.
If you go to Engrave mode, you can adjust the Voice column index property on selected notes for local fixes. The numbering starts at 0 for the leftmost column. There are some options under Notation Options > Voices you can experiment with, as well. In this case however, the quickest fix will be to select both up-stem voices, right-click, Voices > Swap Voice Order.