The last time I worked on a Merchantman was about 35 years ago and I can't remember the floor structural layout but I imagine a solution to lowering beams might be to keep the existing attachment layout on the fuselage double-bubble frames but the beams themselves would have their top flanges 2" lower.
A very wide and shallow 'U' shape with the vertical flanges being attached to the frames if you like. (____________) instead of the conventional (--------------------)
Of course it might be nothing like that!