I don't want to manage that many files. I'll fully admit that I'll hit my limits before the computer cares.

Same here, but the problem is bigger than that. Having to manage a ton of tiny files makes it easier to lose tiny bits of data. What happens if a file changes, gets overwritten and you don't notice? It's much easier to 'version' a single larger file than many hundreds (thousands?) of tiny files containing 4-5 lines at most.