It's not his decision, he made a post saying he really wanted to do the Tour, but the team had other plansI am a bit surprised that Pedersen opted out of the Tour especially after having to abandon it in 2024 but I actually don't think its a bad decision because 2025 Giro has lots of stages that suit him so he should have a decent chance of taking ciclamino and in the Vuelta there are also several stages that he can contest plus the points jersey too.
Milan to the Tour makes sense as he is one of the three best sprinters in the world and can still be very competitive without a Pedersen lead out and I suppose Nys will get his chance in the hilly stages.