You sound like you have never worked in the business world before. Half of business is picking up on tone, ambiguous phrasing, and empty promises with smiles. Reading between the lines is a core part of interpreting meaning, and it why many people with autism spectrum disorders really struggle with things like sales, or people management (at least from the customer or employee's side). Nuance is everything here.

If my boss chucks an ellipsis at the end of the message, does that mean he wants me to....

Answer an implied question?

Wait for him to keep writing more information?

That he wants me to justify what he has just said?

It is not a choice as you argue, to interpret meaning behind ambiguous communication, and have effective communication. I cannot ignore implied tone, because I 'don't have 100% certainty of their intention'