Fixed crown height, single crown fork, you are right.
Cutting the bottom will sharpen head angle.

It really depends on your point of reference as to where the frame moves.
Starting with the top of the frame lined up with the bottom of the top crown, there is X head angle.
Cutting the top off the frame, you need to lift the frame to make that top line up with the bottom of the upper crown again.

The same is true if using the starting point of the bottom of the crown as you just stated.
The bottom of the head tube/stack is the same as the top of the bottom crown and you have Y head angle.
Cutting the bottom changes the point of referance on the frame and so you have a sharper head angle.

In reading your post 1 thing did occur to me.
That is that we are starting from different reference points.
I'm starting from everything lined up at the top side and you are starting with everything lined up at the bottom side.
This difference will make the opposite true or untrue to each depending on where you start from and make 2 (or more) grown adults debate pretty harshly when saying the same things with in the same principals.

Think about it.
What was the original head angle and at what height?
We don't know as the bike wasn't assembled yet. The difference is going to be approximately 1/4" to 3/8" and so the angle is going to be altered very little.
Little enough that it will probably never be noticed. A different brand fork with the same travel will have a different height difference than what we are talking about.
So which starting point is correct?

As being a DH rider, I've normally set up as slack as possible making my starting points at the bottom of the upper clamp and lining the head and all up to there.
In "our world" for lack of a better term, this is the propper set up and starting point.
We would line up to the top side and then cut the top to make it more slack by most available means.

As an XC rider (I'm assuming here, so please correct me if I'm wrong) you've ridden the single crowns primarily, and so your starting point is always fixed at the lower crown.
There fore you would want to start at the lower end and either cut the top in that senerio to not effect head angle, or possible cut the bottom to make it more steep for tighter cornering etc.

In short, I'm wondering if we are hammering at the same point, but from litterally opposite ends of the Stack height.

I do know that either starting point does validate my original point that cutting head tube can and will effect head angle. That is what started this and so Thank you, you actually validated my original point, but from the other end.

Fingers also crossed that we can put this to bed now.