I think break apart alpha already keeps them in order from left to right and top to bottom,
like on Wallace's previous font break apart alpha kept them in order it's reversed like A is at very bottom but they are in order.
EDIT: i just tried with Sans Bold font and break apart by alpha got confused on the order it's all messed up. This script would have to be really smart like character recognition i don't think i can do it.
I was thinking when you're designing your font for custom font, you can just design it over a huge canvas, with guides telling where your characters should sit they don't have to be stack on top of each other for alignment they can sit at different locations all that matters is the layer size or if a vector is defined for it relative to that layer, just have each character on separate layers named A.png B.png, custom font would still work, if you want to view them all at the same time, that .xcf would work too with custom font.