So basically, if the head tube notch is 2.5 cm, the gain in handlebar height compared to a traditional stem on a frame without a head tube notch is 10mm....is that right?
I am not sure exactly what you mean. I think first, it is easier to just substract 2.5 cm to the geometry chart advertised stack. Stem/handlebar vertical stack is an independant matter regardless of the frame geometry.
So to keep things simple, I separate the frame geometry from the cockpit setup.
A standard stem has a 40 mm clamp height, but with a 125 mm / -9° setup, the downward angle drops the effective rise (measured from the top of the handlebar where your hands rest) so it acts more like a 20 mm stack above the spacers.
The Avenger Y-bar has a lower 25 mm clamp height, but its positive rise pushes the total height up to 55 mm (top of handlebar, where your hands rest).
My Winspace T1550 gen 2(size large) had a 560 mm stack +40 mm spacers + 125 mm stem at -9 (20 mm vertical rise) =620 mm at top of handlebar. Same fit would be Avenger size 56 ( 565 mm stack according to the chart, but in reality it is 540 mm due to the notch) + 25 mm spacers + 120 mm stem(55 mm vertical rise)=620 mm at top of handlebar. Both gives me the same effective stack at top of handlebars. I ignore headtube angle because difference are marginal and it simplifies explanation.