Do the Scalar boxes have to face back to back when in use?

While you certainly improve alignment by having them face back to back, the antenna is essentially spheres that have been flattened.

A 3-dimensional sphere would radiate energy in all directions equally.
Being a flat circle, the field shape is slightly altered, although I was not able to find a good visual to show the effect.

Consequently, the boxes do not need to be exactly parallel and equal heights to each other for them to work.

You do want to keep the primary part of the boxes out of the field. Not so much as it won’t work, but keeping the primary coils behind the field, allows them to operate without becoming part of the field directly.

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