Just had a thought about this line from Thufir which led to a few interesting ideas:
Frank Herbert in Dune wrote:“Thufir, old friend,” Paul said, “as you can see, my back is toward no door.”
“The universe is full of doors,” Hawat said.
“Am I my father’s son?” Paul asked.
“More like your grandfather’s,” Hawat rasped. “You’ve his manner and the look of him in your eyes.”
What if he is not, in fact, talking about Leto's father, the Old Duke, but about the Baron? I know this is quite unlikely, but I think it is at least plausible that Thufir, a Mentat, might have worked out in his two years of Harkonnen services that he was Jessica's mother. After all, while Paul says he has "walked the future" and "looked at a record" to know this for certain, he also points out that the clues are there even without prescience.
Frank Herbert in Dune wrote:“When next you find a mirror, study your face—study mine now. The traces are there if you don’t blind yourself.
Look at my hands, the set of my bones. And if none of this convinces you, then take my word for it. I’ve walked the
future, I’ve looked at a record, I’ve seen a place, I have all the data. We’re Harkonnens.”
What if this line is actually Thufir's way of telling Paul that he also knows this, while everyone else present believes him to be talking about the Old Duke? To go deeper into this, there is also Thufir's earlier thought about the Baron:
Frank Herbert in Dune wrote:He babbles too much, Hawat thought. He’s not like Leto who could tell me a thing with the lift of an eyebrow or
the wave of a hand. Nor like the Old Duke who could express an entire sentence in the way he accented a single word.
Now look back at the Mentat's later statement to Paul - he says he has the look of his grandfather, who I'm speculating to be the Baron, in his eyes. It seems likely that in this moment, Hawat would be looking into Paul's eyes, examining them and comparing them to the Baron's. I think it is possible that this look in the eyes is Thufir demonstrating how Paul is closer to the Baron than his father (and other grandfather). Like them, he is expressing a much deeper meaning (see below) in the theoretical look in the eyes accompanying his statement, in the same manner as Leto's "lift of an eyebrow or wave of a hand" or the Old Duke's meaning in his accent.
In this way, he is showing Paul by the example of a mere look in the eyes what sets him apart from Leto and closer to the Baron, because Paul too lacks this ability for expressing things in this way. If we take this to be the case, it also adds another layer to the passage immediately following this:
Frank Herbert in Dune wrote:“Yet I’m my father’s son,” Paul said. “For I say to you, Thufir, that in payment for your years of service to my family you may now ask anything you wish of me. Anything at all. Do you need my life now, Thufir? It is yours.” Paul stepped forward a pace, hands at his side, seeing the look of awareness grow in Hawat’s eyes.
Perhaps this action from Paul is not only in payment for Thufir's "years of service" to his family, as he says, but in recognition of Thufir's message and recognition that he is far from the "true" Atreides that his father was, and that Hawat has every right to kill him as the Emperor orders for this reason as well, mirroring the Mentat's earlier thoughts of slaying the Baron. After all, the idea that Paul is a Harkonnen is later expressed by Bijaz to the first Duncan ghola in the next book:
Frank Herbert in Dune Messiah wrote:“You think of Beast Rabban, the vile Harkonnen, and you glare,” Bijaz said. “You are like the Fremen in this. When words fail, the sword is always at hand, eh? You think of the torture inflicted upon your family by the Harkonnens. And, through his mother, your precious Paul is a Harkonnen! You would not find it difficult to slay a Harkonnen, now would you?”
Now, of course, he just mean this in the sense of his relation to the Baron, and this is just all part of the Tleilaxu plan and getting Duncan to kill Paul, but this could be a deeper message from Frank by putting this line here as well in such a manner to express that Paul is a Harkonnen on a deeper level than just being Jessica's daughter.
Going back to the last chapter of Dune, if we take the whole Thufir idea to be true, it also adds another dimension to a passage concerning Fenring and Shaddam later in the chapter, in which Shaddam similarly expresses what he wishes Fenring to do by just looking into his eyes:
Frank Herbert in Dune wrote:The Emperor turned, looked at Count Fenring. The Count met his stare—gray eyes against green. The thought lay there clearly between them, their association so long that understanding could be achieved with a glance. Kill this upstart for me, the Emperor was saying. The Atreides is young and resourceful, yes—but he is also tired from long effort and he’d be no match for you, anyway. Call him out now ... you know the way of it. Kill him.
In the following passage, Paul feels a "deep compassion" for the Count flowing through him, "the first sense of brotherhood he'd ever experienced." If the comparison between the interaction between Thufir and Paul and the Emperor and Fenring is at all intentional, then Frank has crafted the connection between them even better.
I know that all of this is more than a little far-fetched, but I find it interesting to speculate on these things and I think this in an interesting interpretation.