It's mostly a matter of preference, and of whether the primary chain was just replaced. With the old primary chain still inside you can easily set the chain over the crankshaft, lay it in the bottom, then fit in the primary drive sprocket and its shaft.
If the chain is new, I've found doing things upside down is a little easier to assemble because the primary drive sprocket will sit upright and make inserting the primary shaft easy enough, and the transmission is then easier to reassemble as you are laying the gearshafts into the shift forks and not trying to stand on your head while they dangle down on the tranny shafts siting in the lower case.
When you study the design, based on how the 2 smaller tranny bearings are pinned in the upper case, it becomes apparent that Honda assembled them upside-down, too. Otherwise they would have moved those locator pins to the bottom case, as it is difficult to make those fit into place while holding up the upper case's weight.
