As illustrated below, the boot doesn't have anything to do with the shock body itself. There is no seal or fastener in this case. You may be thinking of off-road shocks where the dust boot is physically fixed to the shock body, or like a boot on the end of a steer rack, but this is quite different, as it serves a different purpose.
The left most illustration is a strut at rest, half way through travel, (so car parked on the street). The boot has fallen, and is resting on the top of the shock, creating the noise. This is technically not exactly what is happening, but I don't have time to get into an animated illustration tonight, so we'll go with the Mickey Mouse version. As the bright red shock body travels up and down, it will carry the boot with it, and occasionally on sharper impacts "clunk" into it, creating the noise.
The middle illustration is a fully extended shock, as viewed in my original photographs. Here you see how the shock can come out of the boot, once the boot is secured to the top plate.
The right illustration shows the car back off the hoist, and the boot secured. The shock body has a clearance between it and the boot, so that they do not generally touch, or cause problems. The boot is there for protection, for shielding, but not for sealing. The bump stop inside the boot is what makes the noise, the boot is just a thin plastic cover.
The green is the top plate (spring hat), brown is bump stop, black is boot cut away, blue is shock rod, red is shock body.
The gap I have illustrated between the bump stop and shock rod is the unintentional gap created by the change in temperatures/tolerances that allows the boot/bumpstop to fall in the first place. Kia intended (as most other manufacturers have) to have a tighter fit in there, so it would naturally keep itself raised.
I hope this clears up not only the functions of the parts involved, but that Kia didn't neglect a fastener, nor did anything wear out... this is a simple case of a manufacturing tolerance being exceeded and by an amount measured in tenths of thousands of an inch. Literally, a hair.
