Yeah, it's unquestionably tracked what exact portions of a YT video your browser actually loads and plays. All playback is controlled by JS and there's no reason YT doesn't hook into those actions and record metrics of every play/pause/seek/mute/etc. user action (in addition to actual network requests made by the browser).
So YouTube has no idea that the content was skipped by SponsorBlock? I find that hard to believe.