Using simple comparison to visualize overlap between two curves results in low overlap values being sorted to the end of the array

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I'm using a simple comparison to visualize the overlap between two curves.
y_d = [y2(y2<y1) y1(y1<y2)];
However, it seems as though all the sections with near-zero overlap (orange curve is on the order of 10E-7) are sorted to the end of the array, completely shifting the whole thing out of alignment.
I've realised that this method essentially creates two lists - the points where y1>y2 and the points where y2>y1, and then simply concatenates them together.
Are there any alternative methods that would conserve the relative positions of the points?

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