I hear what you're saying, but would remind you, first of all, that "deep into conspiracy theories" is the first objection people make when you suggest that LA, his team, a bunch of doctors, a Swiss lab, and the UCI all worked together over seven years to ensure that LA won the Tour without failing a drug test (or without being caught). From non-Clinicians the usual response is, "Come on, you don't really expect me to believe that, do you?"
Behind every human misdeed involving more than one person lies a conspiracy. By definition. So "deep into conspiracy theories" means absolutely zilch.
As for Armstrong complicity in the Contador positive: As someone else explained above, they couldn't have AC going positive while he was on their team, for their own reasons. The following year, when he was on a different team, was a different story. But why then was UCI so slow? For one thing, the UCI is no monolith; one corrupt guy there may not know what another corrupt guy there is doing. Second, AC is a huge figure in pro cycling, arguably second only to Armstrong. So even though you've stuck the knife in him with one hand, it would be important to comfort him and appear to be trying to help him with the other . . . .