I thought the goal of delidding was to directly connect the die to the cooler and bypass the IHS ?
Most cooling solutions are designed around having an IHS. So unless you're willing to modify the cooling solution as well, you're going to have at least a few millimeters of gap between the cooling solution and the die. Not to mention part of the IHS is to spread mechanical stress from the cooling solution to ensure sufficient contact without risk of cracking the die due to how much you're tightening the thing to it.
However de8auer was notable in figuring out that when Intel was using thermal paste as the die/IHS TIM, the spacing Intel shipped the CPUs out with was a hair larger than it could've been (probably due to overzealous application of the glue used). So delidding during this time was to reduce the spacing.