Hi fullstopslash, yeah the idea here is that as soon as a character exists on a given higher layer, that cell uses its own background color, which cannot itself be transparent since by definition a transparent background color means a given cell is completely invisible (including its character).
So if your goal is, for example, to set a glyph on a higher layer but have its background color match some solid background color on a layer below it, then you have to do the matching manually.
Cell contents work as a whole unit, rather than individually. (And probably the more confusing/unexpected part here when first starting to work with multiple layers and transparency is that even with the background color disabled, black will be the default background color for a new cell on a higher layer, since you must have some color for the glyph to be visible at all.)
