Another option would be two Y beams instead of one with enough space to fit the screw between them. Generally speaking the wider the spacing between your bearings, the smaller the effect of slack or looseness in the bearings.
To exaggerate if you have two bearings 1 ft apart and 0.012" slop in the bearings you would see much more movement at the spindle tip than if the bearings were 12 feet apart with the same slop. That being said the kind of linear bearings you are showing tend to be very precise.
My personal preference is to have the bearings as close to the Z-axis as possible and as far apart vertically as reasonable. These things are always constrained by the specific design and the wallet.
Alan
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