Communism is not centralized means of production. In theory it is the opposite: expropriate the means of production from the economic and political elite in order to enable workers to produce what they need and keep their production without getting exploitated. Anyway, we do have seen authoritarian so called "communist" regimes which are indeed centralized in many ways.
On the other hand, capitalism as the defense of private property and free market in theory offers descentralization, through personal freedom, as you say. However we do see that capitalism tends to the concentration of wealth in the hands of a few, thus concentrating power, means of production, the capacity to expropriate personal work from vulnerable workers that don't own capital but only their bodies and capacity to work. Without going too far look at the whales in steemit/hive. They hold lots of power and get to decide what content is rewarded the most and what projects survive. So even though we do have the freedom to post whatever we want and profit from it, the whales rewards condition the production of content. I've seen producers going out of steemit/hive because the didn't get any rewards at all, or I've also seen people making certain types of content just to get more rewards, even though that content is not what they like.
So, centralization does not come from communism or capitalism. It comes from hierarchies that are sustained with power. Power can come from violence (dictatorships came from violent revolutions), capitalist relations of production (which is solidified violence from primitive appropriation), statism (government's monopoly on violence), simple difference in talent or force, etc. Centralization is always a possibility because concentration of power is always a possibility in groups of humans.
So the dynamic of centralization is seen everywhere. Maybe because there are more capitalist countries, we see it way more on capitalism and of course the few communist regimes do show centralization as well.
You are correct - but communism on scale cannot be achieved without massive bureaucracy - ergo more and more centralized with each layer. (hence crony capitalism and oligarchy, with bigger government).
Theory and reality are different that's very true.
Capitalism is the closet thing to a 'natural system' than any other (minus the corruption through monopoly - caused by bureaucracy)
decentralization with free market capitalism and minimal government of any kind, is the best way forward, imo.