[ossiblue]

Kind of hard to tell from your photo, but the boot that is on the thin line doesn't look to be the correct size for the hole--the boot looks too large--yet, the boot looks too small for the large hole to the left. Could be the camera angle though. If the boot fits the hole the line exits, then that's most likely the correct passage and the other cable or line is misdirected. Obviously the boot only accomodates one line.
I don't think, if it's a speedo cable, that it fits into the other hole you identified. I've never worked with a speedo cable but I don't believe the nut is removable on either end so it wouldn't fit through the opening. It actually looks to belong where it is in the photo and the thin line is misplaced.
Just my observations. Someone who knows for sure will respond soon and clear up the mystery.