All of the plant can absorb water. Clones get their water from two places, the substrate and the air. If the top of the plant is covered in water, then because most of the plant is above-ground, the vast majority of its water comes from the top. Roots need two things to grow, high moisture and darkness. When clones get as much as or more water from the top than they do from the below-ground rooting part, then, from the plants' perspectives, their tops are in the high-moisture environment and their bottoms are in the low-moisture environment. If it were to reach out towards the greatest source of water, it would have to be above-ground vegetative growth.
The underground, rooting parts of clones should be kept at even just the slightest bit higher moisture level than their above-ground parts. To accomplish this, there can't be any water on the tops of the plants. The humidity in the cloning chamber is kept a little under 100% and then the plants can feel more moisture where you want them to grow roots.
In addition to where they grow roots, moisture levels also affect whether they grow them at all. If the clones are in 100% humidity, get all the moisture they need while losing none, there's no reason at all to grow roots anywhere. Providing clones just a tiny bit less moisture than they need to survive continuously will help encourage them to reach out roots in search of water.
