Congrats, TK, and a very hearty welcome to Grace!! Hope Mrs. TK is doing well.
First, I have no idea how your lead photo relates to whatever is going on inside your head but I have to say that if it was me, I would tell the forum to go to hell while I fell in love with my brand new daughter! Man, I would spoil that little girl - lucky she isn't mine.
For what it's worth, I agree that it makes more sense to align the headstock with the ways and then align the headstock to the tailstock. That's the way the rest of the world does it, at least to my knowledge. Maybe Matt knows something the rest of us don't.
As for why you got a reverse taper, I'm not sure. You've created a constrained system with a follow rest and are taking a healthy cut with a carbide insert tool on a hardish work piece so I have no idea what the results mean. If you had taken a 6-8" long, 1" OD piece of soft steel, like 12L14, and indicated it to zero in a 4 jaw, then used a well ground and really sharp HSS tool with a 1/64" nose radius( to minimize deflection) to take a 0.002" depth of cut with no other support or constraints on the rod then I would say the test would probably reflect your headstock alignment.
You're right in that we can drive ourselves crazy chasing things down to tenths. Most of the time it just isn't necessary. However, in the case of headstock alignment, it isn't a bad idea to get it as close to zero as you can because you will use that to align the tailstock.
Now, I have to ask you, why are you still reading this? Go kiss your daughter!!