The same instruction is in our SM manual with the Yanmar engine, so I doubt it's a Volvo issue. I think the 54 has the same Vetus exhaust setup as the SM.
We certainly do it when sailing passages, particularly important when on starboard tack for long periods as the exhaust outlet is buried in the water.
Personally I wouldn't put much faith in the flap valve (I hesitate to call it a one-way valve - it's more one way than the other but by no means water tight) 
Cheers
Alan
Elyse SM437