I agree that manipulating Bob makes it hard to rely on Bob for "sanity checks" of my motives, and that that's a significant loss if Bob would otherwise have been useful in that capacity.

And I can sorta see how it might be true in some cases that manipulating Bob might render him more manipulable by others, and therefore less valuable to me, than he would have been had I not manipulated him. (I have trouble coming up with a non-contrived example, though, so I'm not convinced.)

So, yes, agreed: in cases like those, it makes things worse.