Normalized cross correlation via FHT - how can I get correlation score?
Ok, I finally found the reason for my confusion - thanks to this answer.

There were a number of reasons why I couldn't get my spatial NCC and frequency domain peak values to agree numerically. Some obvious, some subtle, all stupid. For the sake of completeness, here they are:


I had missed an offset and scale factor that was introduced when
normalising my image data after importing the pixel values in
preparation for FHT. 
I was using a predicted maximum value for the
    peak, from my sub-pixel shift calculation instead of the actual
    peak.
I had a low-pass filter in the pipeline, which - for
    performance - I was applying concurrently with the correlation
    operation. So my peak value was scaled by the filter.


Not being mathematically inclined, I was wrongly attempting to "explain" my problem by assuming that using FHT was somehow inherently different to using FFT. After being pointed in the right direction I found the above issues and finally got the results I was expecting.