I have already stated above, that due to difference in viscosity, the model that the slicer uses to calculate the extrusion doesn’t always work. You’re assuming that the slicer’s prediction of extrusion is 100% accurate, which in real world it’s not the case. Yes, the slicer indeed tells the extruder to make less extrusion, but that doesn’t mean that over or under extrusion doesn’t come into play when you modify the layer height too much.
What you think the relationship is like:
What in reality, the relationship is like:
Thermoplastic is a complex thing. Real world isn’t always that ideal. At least not for the affordable filaments that we use everyday.