I think the short answer is that as English as no clear way of indicating groupings and sub-groupings in a hierarchical structure, any such sentence has the potential to be confusing. In a computer language we could clearly say, "if condition1 then if condition2 then X1 else X2 endif else Y" or some such. But English isn't so precise. In a specific example it might be clear from context.
For example: "We'll either paint the walls, either blue or green, or we'll tear them down." I think it's pretty clear that tearing them down is not a color of paint, etc, so there's no ambiguity.
But, "We'll either paint the walls or we'll put on wallpaper, either blue or green." Do the colors refer to wallpaper or to both paint and wallpaper? Probably not to just paint or we wouldn't have put it at the end.
Or, "We'll either get someone from accounting to look at this, either Bob or Sally, or maybe we'll ask Joe for help." From the fact that there are two "either"'s, I'd think "ask Joe" is an alternative "get someone from accounting". But the fact that three people are named lures one into thinking that Bob, Sally, and Joe might all be "someone from accounting".