apt.conf (as the name says) contains options for the APT package manager, like proxy configuration, pinning values for different repositories, general configuration (for example not to install Recommend, ...).
sources.list contains only the repository configuration (addresses and which sub-repos to use, but not packages). main, contrib and non-free are such sub-repositories.
APT does not "call" any of those files, they are merely configuration files, not scripts.
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