Giro d'Italia Giro d‘Italia 2024 Stage 3, Novara-Fossano, 166 km

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I think you need a maths lesson. Pog gained two seconds, Thomas one. The gap is the same as if Pog had won the sprint and Thomas had come second.
I think for Thomas the gap to the other GC riders might be more important than the gap to Pogacar...

And because of Swift he lost an additional second to all other GC riders while, as you said, the gap to Pog would have stayed the same.

EDIT: also if I'm not mistaken, tobydawq gets quite a lot of maths lessons. He even gives them.