The problem being solved essentially is: you have two binary strings, and you want to offset one of them so that they match up the best. For each offset, you're taking a dot product of one sequence with the offset version of the other. This is the same as computing the convolution of the two sequences together (https://en.wikipedia.org/wiki/Convolution). Computing this naively would be O(n^2) (doing linear work for each possible offset).
One property of the Fourier transform is that convolution in the time domain corresponds to element-wise multiplication in the frequency domain (https://en.wikipedia.org/wiki/Convolution_theorem), so you can compute the convolution efficiently by taking the FFT of both series, doing element-wise multiplication, and then taking the inverse FFT of the result.
One property of the Fourier transform is that convolution in the time domain corresponds to element-wise multiplication in the frequency domain (https://en.wikipedia.org/wiki/Convolution_theorem), so you can compute the convolution efficiently by taking the FFT of both series, doing element-wise multiplication, and then taking the inverse FFT of the result.