There's a lot of up/down/cw/ccw in that post and my brain may need a second run through to orient, but I think what you're seeing is that using the laser boresighter is effectively the exact opposite of how normal zeroing works, I think.
Boresighter, you're holding the gun alignment constant and bringing the dot to match.
"normal" sight-in, you're going to hold the dot/reticle in the same spot on the target and by adjusting the optic, bring the gun's bore in alignment. And that's how the instructions are written.
That's why it feels backwards. Sort of like if you had a gun with all adjustment via the front sight, versus all the adjustment via the rear sight.