I can't measure the distance between the spoke holes and the axle/bearings, or at least I don't know how to do it with calipers. But I am assuming that if the CNC lathe cut the bore hole for the bearings to go into, and did a final pass over the flange in the same cutting session, then the flange should be centered to the axle. That's why I am assuming that because the spoke holes aren't centered to the flange, that the spoke holes are also not centered to the axle. But I could be mistaken. The only way I know of to confirm whether the holes are centered to the axle, is to take out the bearings so that I can get the calipers in there to take a measurement. But if I knock out the bearings now, I'd have to go and buy some replacements.
Assuming that the spoke holes are +/- 0.25mm offset from the axle, what problems would there be? The spoke tension should true the wheel. But I assume the tensions will be different from one quadrant to another due to slightly different spoke angles and lengths.
I think the bearings are already seated all the way into the bore holes. One side is probably not bored as deep as the other. I suspect this because all the other axial dimensions of the end caps, axle, and shoulders all have 0.15 in them, which is probably the lateral tolerance that the factory uses. But I'll try making bearing presses/drifts to see if I can press the bearings any further in.
I also I have a different OEM hub of a similar design that's probably all made in the same factory, and that hub also has one bearing 0.15mm further in and the other bearing 0.15mm further out. I took the bearings out and put new ones in, and they still had the same offset. Although both were inset either 1.4mm or 1.7mm in past the face of the hub body, so I don't think it made a practical difference.