The explanation here is similar to the Cartesian vs Polar coordinate system.
I think that, for most people, the Cartesian coordinate system is the most intuitive. You move linearly some distance, then linearly some other distance, etc. The ending X/Y coordinates are related linearly to the distances you traveled initially.
In Polar coordinates, you turn some angle $\theta$, and then "walk" out some distance $r$ from the origin. In the end, the X/Y coordinates are not linear; the ending positions is given by $(r\cos{\theta},r\sin{\theta})$. You still have two degrees of freedom, but it's harder to inituitively know where the ending position is without practice, and each degree of freedom - $r$ and $\theta$ - can move both the x- and y-coordinate.
Similarly, you could have a robot with three linear actuators to navigate an end effector to an X/Y/Z spot in space. This is intuitive - the ending position is the distance traveled on each axis.
A robot like the one you mention is like polar coordinates for 3D space - this is referred to as a "spherical" coordinate system. In spherical coordinates you have two angles and a distance. Imagine pointing at the sun - you point SE or SW (azimuth angle) to the sun's projection on the horizon, then you point "up" (elevation angle) to where the sun's height is in the sky, then the sun is some distance $r$ away from you.
The robot you link doesn't have a means to telescope its arm, so instead of a true spherical coordinate system ($\theta,\phi,r$), you wind up with a purely angular coordinate system. Link distances still exist though, so it is possible to reach most coordinates within a sphere of radius $r_{\mbox{sphere}} = r_1 + r_2$, where $r_N$ is the length of each arm segment. It is most coordinates and not all coordinates because, if the arms are not the same length, then it cannot reach an interior sphere of radius $r_{\mbox{interior}} = \mbox{abs}(r_1 - r_2)$.
You are correct in that, if two axes are aligned, then one degree of freedom becomes essentially redundant and you get into a condition referred to as gimbal lock.
For an example, consider only two rotational degrees of freedom for a moment. Each has an arm of length $r_N$. Motion in the plane for the end effector is the sum of the motions of each arm link because the two arms are connected (read about vector addition for more information).
So, the first actuator moves some rotation $\theta_1$. This moves the end of the first arm link to a position of $(r_1 \cos{\theta_1}, r_1 \sin{\theta_1})$. The second actuator is located at the end of the first arm link. It rotates some other angle $\theta_2$, putting the end of the second link at a position of $((r_2 \cos{\theta_2}, r_2 \sin{\theta_2})$ RELATIVE TO the end of the first link. This means that the end effector is actually at:
$$
x = r_1 \cos{\theta_1} + r_2 \cos{\theta_2} \\
y = r_1 \sin{\theta_1} + r_2 \sin{\theta_2} \\
$$
In this way, you can vary $\theta_1$ and $\theta_2$ to add or subtract portions of $r_1$ and $r_2$ to achieve the desired $<x,y>$ positions. The third actuator sweeps that position around the y-axis to achieve the desired location in 3D space.