Hmm... that is interesting.
I've noticed most OEMs (tomos, peugeot, honda) sell the cases- oe replacement- with the bearings installed, making me think there is a reason for that.
my guess was that it is easier at the factory to put the seals and bearings in the cases first with a press, and do the crank later. The big problem i see with those factory tools is that they are pulling across the bearing itself. Might be OK for german bearings running at low RPM but i just try to absolutely not ever put pressure across the bearing itself in any motors i build.
my instinct (and the way i've always done it) would be to put the bearings on the crank first because the aluminum expands more and its much easier to ensure they are seated on the crank rather than ensuring they are seated in the aluminum cases. I would think you would want them to seat on the crank fully and if they have to float, let them float in the case.
plus having more expansion in the aluminum gives you more wiggle room to put the case on with the bearings in situ on the crank, if you are trying to put the crank into the bearing in the cases it is harder to keep everything aligned.
Usually my method is to put both bearings on the crank first, then do one case half, then cool the case half and crank together, apply the gasket or sealant to the cool half so it doesn't start to gum up prematurely, then apply the other hot case half.
I've had way more bearings stick to cranks while dropping them on, than bearings stick into cases... the only cases i ever have trouble with are minarelli and garelli because you have to get all that stupid pedal gear junk aligned before final assy.
usually with those spaghetti motors i end up having to do a slight re-heat of the bearing race area with a bernz-o torch and a couple light taps with a rubber mallet to free everything up.