They have the same package cache, it is just that only the software center trims it automatically.
man eopkg
delete-cache (dc)
Clear out any temporary caches still held by `eopkg` for downloads
and package files. These are automatically cleared when using the
Software Centre but you must manually invoke `dc` if you only use
the CLI approach to software management.
Key word is only use the CLI. So if you use both, it'll still get triggered when using the software center.