Just thinking out loud (dual iso is about a year old, so probably a lot has already been discussed in developing it, so sorry if things already have been suggested

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"I've interpolated the two images with a very simple algorithm"
I don't see the need for comparing two exact overlays pixel by pixel

(probably missing something important here

)
If I did know nothing about dual iso and someone gave me one of those raw dual iso images with the question to gave the brightness difference between the dark and light lines, I would do something like this:
-read the amount of dark pixels (let's say 10 megapixels) and sort them in order of value, plus throw out all values below 100(for example),let's say 100.000 pixels are thrown away because they are too low in value.
-read the amount of bright pixels (the other 10 megapixels) and sort them in order of value, plus throw out all values above 15000(for example), let's say 200.000 pixels are thrown away because they are too high in value.
So you end up with two strings of numbers ( 100, 100, 100, 101, 101, 110...14322, 14322, 14355 etc,)
Now compensate for throwing away pixels.
For the bright value string, discard the first 100.000 numbers in the string (assuming they are sorted out on value, this throws away the 100.000 darkest pixels in the bright image)
For the dark value string, discard the last 200.000 numbers in the string (assuming they are sorted out on value, this throws away the 200.000 brightest pixels in the dark image)
Now you have 2 strings of values to compare.
Now the difference in average of these 2 strings is the difference in brightness...
EDIT: so no pixel by pixel difference, but the average of all "bright" pixels compared to the average of all "dark" pixels.
But I'm probably overlooking something, because you're using 2 points(mid tones and highlights)
So maybe you can take the median(or average) of the first half of the two strings for mid tone point.
And the median(or average) of the second half of the two strings for highlight point.