I'm not too familiar with them either, have only done them twice, (it was close to being only once as I really didn't want to come back over Pontythingywotsit), but i remembered that the line was there.
Went looking for information, which led me to an old BW cruising guide from 1965 at https://www.plaskynastoncanalgroup.org/app/download/5783009099/Llangollen+Canal.pdf which has instuctions for the locks, but no mention of the line. So it would seem to be a modern thing rather than how the locks were originally built.
I wondered if it's due to a pound being lowered sometime after 1965. I doubt that the pound above the locks would have been just because of it's length. Just below the staircase is a "modern" bridge for the A41, which appears to have fairly low headroom, so I wondered if the pound below the staircase was lowered at that time , but the photo at https://www.geograph.org.uk/photo/1392244 from 1965 seems to be a flat bridge, https://www.geograph.org.uk/photo/5270604 being a more recent photo. Also the falls of the staircase and the three individual locks quoted in both the old BW guide and my more recent Nicholsons are the same.
So I'm confused as to whether it is due to one of the lower chambers being deeper, but if it is, I don't think it was by design but a "solution" to a problem that appeared sometime before I was there in about 2005.