Answer
There isn't a single system-wide 'default From email per Company' setting — the practical approach is to set up a separate Email-sending Event Action for each Company, each one hardcoded with that Company's specific From address, and each scoped with a condition so it only fires when the triggering record's Company matches that specific Company. This works reliably, though it does mean maintaining one Event Action per Company, which can get unwieldy if there are a large number of Companies configured.