I don't see where all this confusion is coming from.
The article says that during the DL, Contador was still heavy and as a result, his performance there suffered.
Nothing in the article suggests he took the clen DURING the race, but plenty to suggest that, after the poor showing, and given the extra kilos he was carrying during the race, that he took the clen after the DL (when he was far less likely to be tested, and when it could be taken in a far more controlled training environment rather than during a stage race).
The DL ended on Sunday, June 13, and the Tour started three weeks later on July 5.
A hard training block the week following the DL, followed by a period to allow the clen to drop below detectable* levels, then a little deposit at the blood bank.
*We still haven't heard a really credible analysis of exactly how much clen would be necessary to achieve measureable weight loss over a short period of time, or just how long that amount would stay in the user's system, or what levels each lab tests too (understanding that there is zero-tolerance).