This topic has been beaten to death. Some people get it, some don't.

Fact is if you have a 1000lb of vehicle weight on a spring, you can preload the spring with spacers (or cranking) up to the 1000lb of preload and the spring behaves the same on compression. The misconception is that the preload gets added to the weight of the vehicle and hence changes the spring rate in some way. In fact, the preload is only a threshold to when the spring will begin to compress and the vehicle weight is always vastly above this threshold.

Here is my theory as to why the ride is stiffer when you crank or space a coil. By doing this you change the angle of the A-arms and suspension components (including swaybar components, axles and steering rods etc.) What makes the ride stiffer is that those components no longer travel in the optimal way that the Toyota engineers meant.

What do I mean by this?
The wheel no longer travels straight up on compression. It might travel outward initially as it goes up and then inward after the arm reaches level. This causes increased friction with the ground and increased angular acceleration (inertia).
The axles travel outward in the tulip and then inward as travel continues. The steering rod changes length because the tie rods don't remain at the same angle. This changes toe angle. The other components and links also operate in less than ideal angles.

This may not sound significant but they all add up to more friction in the suspension. This means more force is transmitted to the chassis instead of being absorbed in the unsprung components. A coil or torsion suspension has very little friction compared to a leaf setup. Therefore slight changes in friction are very readily noticed.

What do you think?