Employee A reading email X does not scale. Google reading everyone's email with ever-better AI systems does scale, and is a much bigger threat to freedom, political or economical.
Yes, he does: he looks up the people he knows about.
There is nothing to say these "big data silos" will run "slowly." And even if they ran slowly, the impact they could have on your life would likely be far larger than the more immediate impact of an employee reading your email.
If Google can read all Gmail users' emails, Fastmail can read all their users' emails.