The hub design has the bearing opposite the retained one "floating" to self-align the races. Honda does leave the bores too tight for that to really work: maybe they have a good reason - but I don't know it.
If you drive the free bearing in by its outer race until the inner races are tight on the spacer, both bearings will be out of alignment with the inner races moved outwards from ideal. Both bearings will then be loaded axially - they don't like that, and will wear out rapidly (still takes quite a long time actually, rapidly compared to properly aligned bearings).
If you drive it in the last little bit by the inner race, the bearings will end up properly aligned but it's somewhat abusive to the bearings. using the axle as a slide hammer is the easiest way to do this, take it easy and stop as soon as the inner races are on the spacer with some force along the axle.
You can also drive the free bearing in by the outer race, but for the last few mm stand the hub/wheel on the axle with the retained bearing inner hub against a spacer. Same thing, a bit abusive but with these methods the bearings are misaligned in the same direction during installation - so the races will be aligned in normal radial load riding.
Or just open up the hub bore with wet/dry paper until your bearing is a snug sliding fit. Try to set the free bearing as close as possible to "right" but the bearings will self-align quickly when ridden, and continue to self-align themselves with temperature changes.