Z axis bearing arrangement
Arrangement A: With rails on the moving plate (Z axis) the lower bearing is always as close as possible to end of the tool.

Arrangement B: With rails on the stationary plate (Y axis) the lower bearing is much further away from the end of the tool (vs arrangement A) when cutting close to the home position / tall parts. This is less stiff an arrangement Vs arrangement A. However, when cutting at full stretch near the table than they are the same.

So sometimes they are the same, and sometimes A wins in terms of stiffness, depending on the height of the part you are machining.

I've seen arguments made that arrangement B is OK, probably on small Z travel machines, and that it could be said to be a bit easier to build. Jazzcnc put forward an argument for B, can't remember what it was now. My personal preference is A.

Ballscrew 'preload'

"Ballscrews with preload torque" ? You put this right after the sentence over rails and bearings so assume you mean preload on the bearing carriage- the part which slides on the rail? If so ZA is better than Z0 if you have the choice:
http://www.mycncuk.com/threads/9373-...r-a-diy-router

If you mean preload on the ballscrew - the part which rotates and drives the axis then for general DIY machine the ball nuts as supplied from China are fine. They typically have 30 - 50 um (0.03 - 0.05 mm) backlash. C7 grade is fine for DIY machine, but if you really want there is a C5 grade:
http://www.mycncuk.com/threads/1558-...curacy-V-Price