Since the pixel grid and "force pixel alignment" was doing more damage than good I disabled it completely and left only grid snapping enabled.
In this quick test, It's better but it's still not pixel perfect, you can see a slight, subpixel line that separates both brown planes even though they're perfectly aligned with the 2:1 Isometric grid. Furthermore, this gap between planes only appears in the export. I don't see it in the editor when I zoom in.
So I'm a bit stumped here - I can't use the pixel grid and I can only use grid snapping to an extent. Why is this considered "by design" if it doesn't do what it's supposed to?
A short term fix is adding 1-2px outline in the same color as the fill. But it introduces a completely unnecessary complexity requiring me to sync colors for fill and outline, as well as throwing off my measurements and significantly increasing the time I need to edit the tile or create new tiles.