From reading the docs, I thought that main.snake and main2.snake should be equivalent. But when you try to run main.snake, it errors out as if rule_a hadn't been imported from rule_a.snake. If you put that in the Snakefile then it works (main2.snake works).

See it for yourelf by running:

snakemake -p --snakefile main.snake --cores 1
snakemake -p --snakefile main2.snake --cores 1