Is there a way to create a mod that uses schematics to generate custom structures? (Like having it create custom villages all over the world randomly.) Also, can you fill chests/dispensers in a schematic?
The most certain way to do that is to make mods in the mod.learntomod.com/programs area and use the drone blocks to build a custom structure. Check out the skills and drills < learning to program < drones and locations badges on how to build structures using the drone blocks.
You can place a filled chest by: http://forum.learntomod.com/t/placing-a-filled-chest/133529/5
Is it possible to make them spawn all over the world? like villages?
You could use the loop block to make that effect happen, I think. But you'd need to be careful not to accidentally make an endlessly looping mod.