You're right, it is complicated. Luckily for us all, Rebar and WorldEdit are built to be API independent. With some simple porting, we can be up and running on Spout or the official API when the time comes.
It is the same .jar for everything. But I am not the one that maintains the Spout version, so I can't say more than that.
Java only loads classes that you tell it to, so as long as the Spout part never touches the Bukkit part, we're good.