He doesn't necessarily have to be disadvantaged.
Pogacar won Paris-Nice in 2023, but Jumbo won the time trial. In this TTT team time trial tram is more important than the final section.
Pogacar was only able to close the gap because Jumbo had a significant leadover UAE at the first intermediate point. He reduced the gap, but the gap was insurmountable for victory.
Taking Paris-Nice TTT as a reference, a cohesive time trial team remains the most important factor in this discipline. The last rider, in any case, minimizes losses, but if his team isn't the strongest, he's unlikely to win.