Do LensAlign and the camera need to be at the same height?

Not at all.

The important consideration is absolute parallel alignment between the camera sensor and the front LensAlign Focus Target. LensAlign products provide an accurate yet simple way to accomplish this called True Parallel Alignment™ (TPA™). Simply use the TPA sighting system, and you will find that everything comes into alignment despite any height differences. If, for example, the camera is physically higher than LensAlign, the TPA will force the LensAlign to aim upward and the camera downward and parallel alignment will be achieved.

So best answer about height, is to set the camera and tripod so that it is at a comfortable height for you, and the LensAlign and tripod as convenient.

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