As I said, piracy will eventually extend to the theft of energy or raw matter.
Carbon, silicone and iron are easy to come by in space. Actually, given that olivine may be a common material in asteroids you're looking at abundant magnesium, iron, silicone and oxygen right there. However things like rare earth metals may be less easy to come by and if 3D printing jumps to molecular printing, then there'll be ships carrying pure metals as goods. Consider Neodymium cost averages $350/kg, a ship hauling it out to Neptune will be worth a lot of money stolen. Especially when the pirates would be selling for <$300/kg.
If piracy happens over raw materials, eventually so will war even if it's just to stop the pirates. However there'll be asteroids found with thousands of tonnes of easily mineable rare metals, and then we'll see space battles.
When commanding the high energy technology necessary to transmute elements in useful quantities becomes widespread, then all resource contention is going to be about energy. Those with access to more energy will be more powerful. People will covet the bottoms of steep gravity wells and proximity to suns and black holes.
Others will value their freedom more and try to get by with less, and will avoid such political and literal hot spots. The vastness of space will be their most valuable resource. They may well be the final nomads and the last vestiges of humanity.
The logical steps in 3D printing is to increase the number of molecules the printer can print with. There's almost an infinite number of molecules you have to deal with, so it's a very logical step that once 3D printing becomes a commercial endeavour then there'll be quick steps made towards an atomic printer.
91 regularly occurring natural elements is a much shorter order than tens of thousands of common molecules. Considering there are over forty simple hydrocarbons and molecular printers start looking bulky, granted you might only ever use a maximum of 5 hydrocarbons, but that day you need a 6th you'll be cursing your shitty base model printer.
Endless wars over oil, rare earth metals in Africa and the ever increasing price of iron ore would tend to indicate you might be wrong about that.
Just because a single 3D printer won't use much won't magically make resource constraints disappear.