The tunnels do actually start immediately to the west of Stratford station, around Pudding Mill Lane. The new line follows a different route from the existing main line into Liverpool Street - meeting up with the other branch in Stepney and then via the new station at Whitechapel. When trains start travelling through to Paddington they will take this route.

This means that the boundary between the mainline signalling and the new CBTC signalling in the core is at Stratford. But this only applies to trains taking the new route; services on the existing GEML/Shenfield Electric lines continue to use mainline AWS/TPWS signalling, which is why there hasn’t been any impact on services to date.