From what I've read, it appears that OpenGL ES 2.0 isn't anything like OpenGL 2.1, which is what I assumed from before.
What I'm curious to know is whether or not OpenGL 3 is comparable to OpenGL ES 2.0. In other words, given that I'm about to make a game engine for both desktop and Android, are there any differences I should be aware of in particular regarding OpenGL 3.x+ and OpenGL ES 2.0?
This can also include OpenGL 4.x versions as well.
For example, if I start reading this book, am I wasting my time if I plan to port the engine to Android (using NDK of course ;) )?
From what I've read, it appears that OpenGL ES 2.0 isn't anything like OpenGL 2.1, which is what I assumed from before.
Define "isn't anything like" it. Desktop GL 2.1 has a bunch of functions that ES 2.0 doesn't have. But there is a mostly common subset of the two that would work on both (though you'll have to fudge things for texture image loading, because there are some significant differences there).
Desktop GL 3.x provides a lot of functionality that unextended ES 2.0 simply does not. Framebuffer objects are core in 3.x, whereas they're extensions in 2.0 (and even then, you only get one destination image without another extension). There's transform feedback, integer textures, uniform buffer objects, and geometry shaders. These are all specific hardware features that either aren't available in ES 2.0, or are only available via extensions. Some of which may be platform-specific.
But there are also some good API convenience features available on desktop GL 3.x. Explicit attribute locations (layout(location=#)), VAOs, etc.
For example, if I start reading this book, am I wasting my time if I plan to port the engine to Android (using NDK of course ;) )?
It rather depends on how much work you intend to do and what you're prepared to do to make it work. At the very least, you should read up on what OpenGL ES 2.0 does, so that you can know how it differs from desktop GL.
It's easy to avoid the actual hardware features. Rendering to texture (or to multiple textures) is something that is called for by your algorithm. As is transform feedback, geometry shaders, etc. So how much you need it depends on what you're trying to do, and there may be alternatives depending on the algorithm.
The thing you're more likely to get caught on are the convenience features of desktop GL 3.x. For example:
layout(location = 0) in vec4 position;
This is not possible in ES 2.0. A similar definition would be:
attribute vec4 position;
That would work in ES 2.0, but it would not cause the position attribute to be associated with the attribute index 0. That has to be done via code, using glBindAttribLocation before the program is linked. Desktop GL also allows this, but the book you linked to doesn't do it. For obvious reasons (it's a 3.3-based book, not one trying to maintain compatibility with older GL versions).
Uniform buffers is another. The book makes liberal use of them, particularly for shared perspective matrices. It's a simple and effective technique for that. But ES 2.0 doesn't have that feature; it only has the per-program uniforms.
Again, you can code to the common subset if you like. That is, you can deliberately forgo using explicit attribute locations, uniform buffers, vertex array objects and the like. But that book isn't exactly going to help you do it either.
Will it be a waste of your time? Well, that book isn't for teaching you the OpenGL 3.3 API (it does do that, but that's not the point). The book teaches you graphics programming; it just so happens to use the 3.3 API. The skills you learn there (except those that are hardware based) transfer to any API or system you're using that involves shaders.
Put it this way: if you don't know graphics programming very much, it doesn't matter what API you use to learn. Once you've mastered the concepts, you can read the various documentation and understand how to apply those concepts to any new API easily enough.