I've started to wonder over the past few years myself: maybe in some cases they very much do, and it's not stupid at all? If you know such emails may come out in case of trouble, then it can in turn become a tool for a low level of whistleblowing/accountability in a hard situation. A lot of us are fortunate enough to not be placed in professional/personal situations where we'd see something with life-safety consequences and not be able to blow the whistle or feel comfortable walking away. But what if one were, or what if the situation is genuinely gray? Like, you get the feeling something may be off the tracks in process, and your management chain/reporting processes aren't responsive, but it's not actually at all clear from your level that it's really important. Maybe it's just you. Sending a "private" email with your concerns to a coworker over official email might be then be a good way to bookmark that. If nothing ever happens it'll forever remain an undiscovered internal email. But if things ever go so wrong that the company actually faces subpoenas from the government over it than there will be a record.
I mean, what you're saying seems to imply that the engineers should have been concerned about keeping Boeing's bad behavior private right? Well, should they? Yeah the company under its modern McDonnell Douglas leadership certainly doesn't want emails like that coming out following the deaths of hundreds of people due to a bunch of company blunders. But I don't think it follows that engineers shouldn't want emails like that coming out. If they're angry enough, they may even actively want such emails to reveal exactly how bad things had gotten internally, in ways that really would embarrass leadership in a newspaper headline or Congressional hearing.