Measure however much water you put in the bottle as the full feed amount. Like you said, it’s only showing more simply because of the thickener in it causing displacement. There is still only 3oz of liquid there.
As the others have said you measure by using the amount of water, just as you would measure your formula scoops based on the amount of water, I know it then looks like more in the bottle but would still count as a 3oz feed
Off topic but what thickener are you using?! My son is on beech nut oatmeal as a thickener for reflux
3oz