OK.
Here's another picture.

C= Max height as defined by the bottom of the upper clamp of the fork.
The top of the head tube/headset bearing can not go above point C for the obvious reasons.

A= Head tube/headset bearing stack height.
B= Allotted space as defined by the 2 clamps on the fork.

Point C on the head tube will not rise above point C on the fork.
This is your fixed point of reference.

To make dimention A the same size of dimention B you must subtract or cut materiel in this case.
By cutting the lower part of the head tube, there is no change in head angle.

Now here is the important part that I think you are missing.
By cutting the top of the head tube you are making point C on the head tube lower than point C on the fork by the exact ammount as the difference in dimention A and Dimention B.

The frame did not move yet.
It still sits too low in the bottom and now also in the top.
So we move the frame up to the level of the opening in-between the 2 crowns and hopefully measured out acurately.

The fork height stayed the same, but we took some materiel off of the top of the head tube.
We had to make the Point C on each the head tube and on the fork match again, so we lift the frame up into position.
It does, in fact, have an effect on head angle.

And PS
I'm not butt hurt Gastro, no need to worry about that.
This has actually turned out to be an interesting debate.
I'm just thinking that it needs to stay to just the issue.

I also don't really care one way or another about F3 or what ever his name will be this week.
He will, in time, either show that he's a good contributing member, or not.
That's up to him, and not mine to judge