First answer is easy to give: the DPA itself states that the government and Boeing's agreement applies only to Boeing and goes on to state expressly that the individuals who were involved remain subject to prosecution. However, whether these two individuals actually will be prosecuted, the avoidance response is to say it's still too soon to forecast . . . but my inclination is to anticipate that despite trenchant efforts by their defense counsel, they will face charges.
Second, the DPA Statement of Facts struck this SLF/attorney as so infuriating that I couldn't even read it sentence-for-sentence. That said, it is striking in that it serves as a predicate for fraud and conspiracy charges. But: the charges involved in the DPA are only those against Boeing relating specifically to the conduct (or misconduct, as the situation may be) spelled out in the Facts. Do I think those Facts could provide part of the basis for prosecution for securities law violations? - possibly a substantial part of such a basis? I do think so (and an anecdote about why, at the end). It's not my area so I won't try to predict any precise claims; but doesn't it sound like the stuff of securities fraud for Boeing to have said, repeatedly, that the return to service was just around the corner? And for FAA to have felt the need, repeatedly, to assure the public that the timetable was going to be set by FAA and not by the planemaker?
Last answer, also mostly straightforward - the DPA is a limited deal, releasing the company just from the charges against it arising from the specific acts and omissions alleged to have been taken by the two individuals. The rest of potential criminal responsibility is left available.
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A few years ago a major U.S. university became immersed in intense publicity and public outrage over a serious, and sickening, scandal arising from a sports team doctor (and faculty member) having engaged in a long-term pattern and series of sexual assaults against young women and girls on various sports teams, including an Olympic team. The victim impact (should be, Survivor impact, but the other term is what is used in court) statements in a courtroom where the jail-jumpsuited doctor had been convicted gripped a nationwide television audience. Having practiced in higher ed, I watched much of this court proceeding.
It seemed odd that the person who was president of the university attended one of the court sessions. She appeared frozen by a sense of impending catastrophe, though laboring mightily to mask it. Confronted by a survivor in the hallway - on t.v. - she only deepened this impression (admittedly subjective though it is).
My point is, when I saw Dennis Muilenburg appear before committees of the United States Congress, both in the House and the Senate, the look on his face, his general demeanor, flashed right back to those courtroom scenes.
It ain't over 'til it's over.