I believe that practicing gap shooting makes you better at instinctive shooting. This is the case because every instinctive shooter is using the gap method, but just using it subconsciously.
For example, if you practice gap shooting at set target distances, your gap acquisition gets extremely fast. Your brain just starts putting the point down X inches on the target. I honestly use both methods. I switch back and forth between gap shooting and instinctive shooting at all distances, so that I can acquire sight pictures faster than consciously finding the correct gap at each distance. Maybe switching back and forth messes some people's instinctive shooting up, but it has only served to improve mine.
Just to add to the discussion, I also print out a small gap table and tape it to the inside top limb of my bow. I can then mentally range the target, glance at the table and get the exact gap I need at that range. [If you know two distances in gap shooting, the point on & max gap, you can calculate the rest of the table using a parabola equation.]
Since I have the gap table on the bow, I can then reverse the process to double check my 'instinctive shooting'. First, I pick a target X yards out, then instinctively draw on it, look at the point in relation to the target and estimate the gap. Then I double check my gap table without ever shooting an arrow. Draw again, get the correct sight picture using the gap method, then let the bow down again. For the actual shot, I will draw and release using 'instinctive shooting', now that my mind is fine tuned for the sight picture at that distance. Done over and over, you automatically gap your shots without thinking about it.