The "interface reference positions" are based on the maximum and minimum of each object in the simulation. This is why you see multiple points at the same location as the maximum of one object is same as the minimum of a different object. You can enable only one of these points (same locations) to be selected as the layer interface in the simulation. For example max(substrate) then min(etch) then max(etch).
Please let me know if you have any further questions.
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