Hi,
I have just built or nearly finished a Crafter 4 motion mwb, yes the 100mm is a pain as by the time you insulate the roof and then build up the floor levelk to a decent insulation value you dont have a lot of roof hieght to play with, i am 5' 9" so it is ok, but if your 6' then forget it unless you skimp on the insulation.
The other issues are external grey waste tanks, you have to have a bespoke one made to fit in the limited space on the drivers side under the sill NAW fabrications made mein and give good advice.
If you fit out a mwb the side pods area must, although i can sleep lengthays due to moving my shower toilet forward, however i do not have a twin seat and table at the front behind the drivers seat, so i use the drivers / passengers seat swivel, which also cuases and issue as the hand brake is higher due to the floor level so i have had to fit an electronic hand brake switch on the dash.
With the Merc you wont have the issues on floor hieght as it is a higher ride, were as VW took the wierd aproach to higher the floor hieght and not increase ground clearance, mad still thats the VW way "if its worth doing, its worth doing in a totaly mad way, rather than follow logic".