I thought Othar was actually in the chronometer as well, but I think it's just weirdly worded? For anybody else I'd say it's a bad turn of phrase referring to how Othar is missing and all that's left of him is the chronometer. But with all the time traveling stuff from Othar's Twitter account, I'm far more inclined to believe that Othar did wind up trapped inside a clock.

On the against side, I'd also be surprised if the Foglios revealed Othar's fate in a filler side story. The people we've seen in the side stories (other than Agatha herself) have generally been fairly minor characters who can safely be revealed to have survived.