I think it partly has to do with the density etc of the cleaning agents, some don't mix well unless introduced at a time where they can get as low into the tanks as possible right from the start, and then get mixed as the fuel gets added, creating a better blending process with the cleaner.
Although most fuel cleaning agents do mix in with the fuel fairly easily, often they take a little extra effort to get fully mixed, and when just poured onto the top of fuel, they could just sit on top of the fuel for some time, before mixing or being absorbed properly.
Fuel itself is made up of many parts, and is blended to get everything to mix properly, part of the reason fuel can go "off" in time is because it's various parts start to separate.
I don't think just the act of driving mixes everything as well either, I have played with the principle of all this in the past, and noticed it takes a much more severe action to mix substances together than what can be created by just driving, and even more so in tanks that have baffles etc designed to dampen the movement of fuel, which can also act to slow the mixing of the fuel.
When I dose my cars I always try to make sure I put the cleaner in first, often at home, then fill up on my way out somewhere.