I have always assembled the cases like that. The only thing to observe is the 3 half rings that locks 3 bearings. They must be seated correctly on bearings. Case will enter and not slide sideways so any of them can fall off while enter the grooves in upper case. You will probably hear if that happen. But it has not happened me.
Honda manual also show upside down assembly. Trickier to get the gear fork in place as I have heard, never tried it.
Upside down can be good when gearbox, with bearings need to be restored with cylinder and head still in place if they are leak free and good condition. Just lift under cover.