Option A is best - the problem with the other one is that the rails (obviously) offer no support parallel to the direction of travel, so when a force is applied parallel to the Y-axis, the lower bearings can move slightly along the rails without the ballnut moving. It wont move very much, but that still means you have a lower stiffness. It's therefore not as strong as having the ballnut directly between the rails.

You should find this document useful:
http://www.thk.com/sites/default/fil...l/a/ee_A15.pdf

Also, depending on the design of the rest of the machine, you may be better off putting the Z-axis rails on the Z-axis plate (which holds the spindle) and the bearings on the Y-axis carraige. It tends to reduce the overhang. I'm not keen on mounting the rails directly to the aluminium extrusion either...