I had a problem with this using the betd bearings - wrote off a crankset in the way you describe - splines not engaged (xtr :(, but a bit past it so no huge loss).
Given that many people do replace the bearings no sweat I'm sure it was something I did wrong, not sure what though. It seemed that the bearing plus seal was too wide, so maybe I hadn't quite pressed it in correctly. I could tell it wasn't quite right, but rode it anyhow which wasn't the most intelligent thing to do. It was also an xtr from a few years back, not sure if it could have been a slightly different size shell.
Anyhow, it sounds like you know what to look out for with respect to seating the bearing properly and engaging the cranks, so I'm sure you'll get it right.