If I'm reading this right, you have an expectation that both bearings will be fully seated. That is incorrect.
Per the service manual, the bearing with the retainer is installed first. This bearing is installed firm against its seat, and then the retainer installed/locked into place.
The spacer is installed, and then the opposing bearing. The opposing bearing is installed just far enough until the spacer is lightly "caught" - with essentially no side preload.
I made this mistake last year (fully seated the non-retained bearing) - and then had to pound the non-retained bearing out, bought a new one, and did it again - the right way.
The bearing and retainer are the parts that position the wheel left to right - in other words, that counterbore is a critical dimension when machining the wheel/hub. The opposing bearing counterbore has no real critical depth tolerance (other than it can't be too shallow).