It comes up automatically with the irons, because you practice with the irons and present the gun the way you were taught or figured out to present it with the irons. The red dot isn't the irons.
I always presented the gun with iron sights with my focus on the target and my front sight. I also tend to push the gun out right away, picking up the front sight as I go and put it on the target.
When I bring the gun up that way, the attitude of the gun is slightly more "muzzle up" due to looking for and focusing on that front sight. If you do that with a dot sight on the gun, you wont see the dot, because its sitting somewhere above the top of the sight (that's where the iron sight alignment is, if you roll your head down and look) and you need to drop the muzzle end to have it appear.
With a dot on the gun, you need to break a couple of habits and instill a couple of new ones. Thats where the learning curve has been for me. It was a lot easier once I saw and understood what was going on and focused on correcting it.
With your focus on the "target", you want to bring the gun up closer in, in front of your face first (instead of pushing out right away) with the muzzle more level or slightly down and you'll pick up the dot more quickly and closer in. Dont push the gun out and then start looking for the dot.
You're also not focusing on the dot, but on the target. If you present the gun right, like you were point shooting the target, the dot will be there, and usually very close to being on target, if not on target. "Point shooting" is a big clue here too.
This may make more sense as far as the presentation goes. The top half of the triangle is the "dot" presentation, and the lower half, using the "irons" presentation trying to pick up the dot.
One thing Im seeing now since I've been focusing on shooting the dots is, my irons are more on target quicker and very close to already being aligned on presentation, as Ive broken that "muzzle up" on presentation habit and Im presenting the gun more muzzle down, like Im shooting the dot.