Sri Jagannath Express is as good as Abada Prasad - Brandon Buffard

One possible reason as to why SCR is not doing the Intermediate block signalling or Auto-signalling on both the bridges is that both are (or were, at least a couple of years ago) operated as twin single lines.
I remember observing the signals at the end of the PF on the KVR side of RJY station. The signal used to have a 'Fast' and 'Slow' line marked. The Fast line was for the Arch bridge and the Slow line was the Road-cum-Rail bridge.
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A few years ago, mostly freights and the passengers halting at Godavari station, used to take the Fast line while going to Kovvur. Afterwards, I guess the Road-cum-Rail bridge had some repairs (it used to have a heavy speed restriction around 2010-12) and the MPS was increased. Even till recently there was a 'Locomotives not to exceed 30KN TE' board in place, which meant that freight locos were to move slowly and some restrictions while operating MU'ed locos (TE - Tractive effort; More TE means more load pulling capacity and more load on tracks).
As far as I know , the MSB-MS section is the only bi-directional section with automatic signalling in IR and the track circuits, arrangements become very complicated. They probably just made them single block sections to spend less effort in managing signalling.