Yes that third line coming from Allahabad via Manduadih is only connected to PF1-3 BSB which is also used by goods,passing trains as well as terminating ones, So normally you can see trains coming into BSB from ALY/GCT side wait for lomger duration at Manduadih/Varanasi City sometimes to the extent of hours just for PF availability.
Trains from ALD can still use the Janghai Bhadohi line via Phaphamau, Prayag to come into BSB avoiding the Manduadih bottleneck.