The angles of the shots are different. It is true that the 'relative' angles on a pool table do not change - a spot shot is always the same angle regardless of the size of the table. But if you take a shot 5 inches off the rail 2 diamonds away from the corner pocket and imagine a triangle - the base of the triangle will always be 5 inches, but the height of the triangle will change the bigger the table gets. 2 diamonds of height is much longer on the 9 foot table than the 7 footer - so the angle has to be different. Taking this analogy further, the angle required to cut said shot to the pocket in a 7 foot table would be an undercut on a 9 footer - as the OP stated. It would come up short. Your brain was trained to hit the 5 inch 2 diamond shot at X angle, and it was slightly off.
When I aim I do not use the diamonds to tell me how thick or thin to cut the ball, I am guessing most people do not do this. I look at the cut angle required to get the ball to the center of the pocket and where that contact point is on the object ball to do that. So for me the angles would not change on different size tables.
Also, if you are looking at it as 2 diamonds from pocket and 2" off of rail you are using 2 different measuring systems. If it is 2 diamonds from the pocket and a 1/2 diamond off of the rail for example then the angles would be the same on different size tables. If this were not the case then spot shots would be different angles on different size tables.