Early on, I found that I could trick myself when shooting "instinctively" at longer distances by focusing on a spot a little higher than I really wanted to hit. This is not really instinctive shooting, since you first either have to know or estimate the distance to the target, and then decide where to focus in order to hit your target.
You can learn to shoot instinctively, or use an aiming device, or switch back and forth between the methods. But you send a mixed message to your brain when you try to blend instinctive shooting and an aiming device into the same shot. When we shoot instinctively, we are not making a conscious decision about where to hold to shoot at various unknown distances; we just focus on the spot we want to hit and rely on our brain/body connection to figure it out based on having shot many arrows at similar distances in the past. When I was trying to shoot instinctively, and purposely focused high, my brain eventually figured the deception out and my arrows began to march upward toward the spot I was focusing on, leading to confusion.
This doesn't happen if we purposely use some aiming device, since we are always telling our brains to line up on some particular point of reference, and the brain never gets a mixed message.
It doesn't happen if we shoot instinctively, since we never make conscious decisions about aiming the shot, so the brain never gets a mixed message.
My advice would be to either shoot instinctively, which means always focusing on the spot you want to hit, and accepting the fact that it will take your brain a while to figure out where to hold the bow at a new distance, or shoot using an aiming device. Either way you're sending a clear message to your brain. It also works to switch between methods, say using instinctive for short shots and an aiming device for longer shots. But trying to combine the methods into one shooting method didn't work well for me, and slowed my progress until I made a clear distinction between the two.