Interesting. It would seem just like Durandal to create a person who expressed such doubt in D's motivations and methodologies. A further test of our loyalty as well, perhaps. But either way, there were certainly BoBs to meet here, and they were doing pretty much what Blake said they would be ... just a shame you didn't leave any for questioning ;).
Also, as you say, things are driven by plot requirements, writing and suspense. We also have to remember that we never hear from Tycho (doubt) again after Mercy. But Thoth does a crappy job of advancing the plot; I've only just come to (understand?) this part of the game ... but I guess the idea was to get us talking about it ... to Infinity, and beyond.