To me at least, having my aimpoint mounted at the end of my upper rail feels better for acquisition than having it closer. Is their a reason for this and if so can someone explain it. I can't seem to figure it out.

I am a new AR owner, so I don't know much about the AR world. But I feel the same way.
Having it further forward allows me to see my target better with both eyes open, and still see the dot.
I have a carry handle rear BUIS (detachable), so I put the scope between that rear, and my front fixed sight, and like the result. I was going to get a flip-up rear BUIS so I could get the scope back farther. But I think I like it forward.

Geometry

When your Aimpoint is right in front of your face it takes up a great deal of your peripheral vision, the farther away from your face you place the sight the less of your peripheral vision is obscured giving you better situational awareness, hence a comforting feeling.

I also like the "far forward" mount.  At the very end of the rail.

I think it's because it doesn't obsure our field of view quite as much, as when it's farther back.  You can see more of the target, and it's surroundings.

I guess this is why.  I know I definitely preferr to have it up front on the upper than farther back.

ETA:  Hopefully someone with a little more "techinical knowledge" can chime in on this. We didn't have red dots when I was an 11B.

I mount mine in the sweet spot depending on the rifle.  I don't want it too close otherwise it takes away from peripheral vision.  If it's too far forward it limits the FOV through the tube.  I like to find the sweet spot where the body of my aimpoint micro T-1 has a ghost ring effect and the body of the scope disappears when aiming with two eyes.

I like mine forward, especially on my coyote rifles.  An often overlooked benefit to the sight moved foward is your less likely to breath on it and fog it up when it's really cold...which by the way it is here right now, 13 degrees!