I am not sure I follow your notation, but it seems that you are taking care of pixel scaling only, and not full-frame noise. It is not clear to me how to estimate frame noise in this approach.
Here is my thinking in more detail:
S and N are exactly the full-frame values used by ImageIntegration currently. In other words, ImageIntegration currently weights all pixels in a frame by (S / N)^2. S is the full-frame measure of scale or dispersion. N is the full-frame measure of noise. Actually II normalized these (S / N)^2 values by reference frame measurements, but this is exactly the same. So this is the full-frame part. In other words, pixels are multiplied by (1 / S) to normalize their dispersions, so noise becomes N / S, and when inverted and squared you get (S / N)^ 2.
The per pixel part is due to F = mean(flat) / flat. This is the scale factor applied to pixels when flat fielding. Because it is multiplicative, per pixel noise becomes F * N after flat fielding.
Combining full-frame and per pixel parts the net scaled noise is F * N / S. And hence the integration weight is (S / (F * N)))^2. Basically ImageIntegration currently uses this formula with F set equal to 1. So to include the per pixel scaling replace the 1 by the flat field information.
Finally, because pixels get registered and interpolated by SA, the F numbers must be processed likewise with the same matrix and the same interpolation scheme, at least I believe so.
My gut feeling on this is that if this works at all, the improvement will be minor, at least on my subs.
Regards,
Mike