I had expected Thomas to take the lead when he managed to close to Jonas Wingfarm & Pogacar. after Pogacar had tested Jonas. at that point it was Thomas that had the most to win by setting a decent pace and gain distance to Bardet and Yates, Quintana, etc, and securing his top3 plateau, but he was likely on the edge and couldn't/wouldn't risk anything.'
The last thing you want is Jonas being the pace controller after Pogacar-move, as Jonas had fabulous Kuss in the back, and had a clear incentive in getting him back whenever he could..