It's not just where the engineers went into a tunnel that counts but where they aimed to come out at the other end. There are a couple of tunnels by Bank Hall on Merseyside that begin near the surface at one end and descend to emerge not o far below the surface at the other end. I think the line descends toward some of the remaining docks.
At Crewe the Independent Lines from Salop Goods descend a little (They're already fairly low compared to the station lines) go into shallow tunnels and climb back up to meet their respective main lines at the other (Down) end. In the opposite direction the Up Independents definitely burrow down to their tunnels. On the Liverpool lines the common level is achieved close to Crewe Coalyard Box.
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