That was meant to work like a venturi, helps midrange, but there is a limit. Honda used to build a 'venturi' into the exhaust passage of their small 2T bikes, but the flange was stiller larger than the port.
Stock 701 porting is about 42mm diameter for exhaust, so 48mm is way oversized - 30%, but look how much grinding a B-pipe manifold/header to 50mm helps even on 701
A well designed piped engine, the Yamaha GP800R, has a port of about 50.5mm diameter and the flange is 48mm, about 10% smaller
10% on a 56mm port = 53mm flange, which is 22% larger than the current flange/manifolds being used
A 1200 with 56mm port and 48mm at flange has the flow area reduced by 36%, going up to 50mm at the flange reduces the deficit to 25%, at 52mm it will be 16%. Difficult to port further than that with current flange layouts
Blair recommends a factor of 1.05(Peak) - 1.125(Broad), look at snowmobile flanges, so according to him a 56mm port should be at least 58.8mm at the flange