This mod sets coal stack size to 100, when my other mod (Space Exploration) is supposed to have it set to 50.

I believe it is due to the following bit of code from data.lua:

if item["wood"].stack_size > item.coal.stack_size then
stack = item["wood"].stack_size
item.coal.stack_size = stack
else
stack = item.coal.stack_size
item["wood"].stack_size = stack
end

If I understand correctly, this is ensuring that the coal and wood stack size are equal to each other, taking the size from whichever of the two was larger. I don't understand why they need to have the same stack size, but could this perhaps be omitted from the mod? Sometimes other mods have more important reasons why the stack sizes should differ. In Space Exploration, coal stack size is reduced to 50 to ensure that shipping it does not become overpowered.

It's there to set the overall energy transport densities relative to one another, so the wood/charcoal/coal fuels have some (minor) distinction, since there's otherwise little reason for coal to exist other than a moderately flavorful intermediate.