Great question!
You might have learned that the amplitude of compression and the amplitude of particle displacements are not synonymous. In fact, the maximum amplitude of pressure and the maximum amplitude of particle displacements are out of phase for $\pi/2$. And twice $\pi/2$ (one for original, and one for the reflected wave) accounts for the missing $\pi$ in the phase change of particle displacement.
Imagine, that rarefaction travels towards the wall, which is on the right side. On the moment the wave strikes the wall, maximum displacement is left of rarefaction, that is $\pi/2$ behind it. The same is true for the reflected wave, that is, maximum displacement is again left of the rarefaction, only the direction of the wave is opposite, so maximum displacement amplitude is $\pi/2$ in front of rarefaction.
Thus, the phase of particle displacement changes phase for $\pi$, while the phase of pressure does not change at all at rigid surface.
I will focus on just a little bit of one of your questions - the relationship between compressibility, density and pressure - and per my comment, recommend that you narrow down the scope of your question.
As you know, in a gas we experience "pressure" because molecules hit the walls of the containing vessel. When I double the number of molecules in the same volume at the same temperature, I double the number of collisions (each imparting on average the same momentum) and thus double the pressure - this is the familiar ideal gas law.
Now when the size of the molecules becomes a sizable fraction of the volume, the rate of collisions goes up. Imagine a pingpong ball between two walls. If the distance between the walls is large compared to the size of the ball, the time for a round trip is inversely proportional to the size of the ball; but as the distance approaches the size of the ball, the rate of collisions goes up rapidly.
I think a similar thing happens with "nearly incompressible" liquids: there is a small amount of space between the molecules, but they are permanently bumping into each other and into the walls of the vessel. As you increase the pressure, they bounce more frequently as they have less far to travel before they collide with another molecule (or the wall).
All this is still treating the liquid like a non-ideal gas. In reality, not only do you have the finite size of the molecules, but also attractive forces between them. Both these things make the picture a bit more complex than I sketched. But I would say that the above reasoning nonetheless applies (with caveats).
As for the experiment you described with stoppers on the inside or outside - there are other things going on there as you go from the static (no flow) to the dynamic (flow) situation - the water needs to accelerate before it will flow out at a certain velocity. But I think all that should be the subject of another question.
Best Answer
Here is what I know:
A wave generated in water is said to be both, transverse as well as longitudinal. Hence vertical and horizontal motion of water molecules, both generate it.
If your stone is an ideal point sized mass then it will create a trough. However, a practical stone will create a trough at center and crest around the submerged part of stone simultaneously (approx).
It forms a circle because the wave propagates in all directions on the surface of water with same speed.