YouTube absolutely can see which parts of videos people are actually engaging with. So can creators. And sponsors can request engagement metrics as part of their sponsorship deals.
Advertisers care about impressions and engagement. A person simply watching a sponsored segment is an impression. If people’s impression metrics for sponsored segments start dropping, they become less attractive to sponsors as they knew they’re going to get fewer impressions as part of the deal.
It may, or may not, be a very small impact but it is an impact nonetheless.
If nobody is watching sponsored segments (which we’ve established: YouTube itsself, creators, and sponsors can track) then companies don’t have any incentive to sponsor videos, and creators no longer get revenue from sponsorships. Sure, this is a very end of the line example, because there’s always going to be someone who doesn’t have sponsorblock installed and can’t be bothered to skip the segment.