Re: Good riddance to old trash...
"OS X is using the Linux kernal (albeit a well outdated one) and what looks to me under the hood, to be a complete Linux operating system in every way."
Apple use a fork of the Mach kernel, a microkernel, completely unrelated to the Linux kernel, which is a monolithic kernel. The kernel and components are provided freely as Darwin, and a few Darwin distributions have existed over the years. There's very little to distinguish them from an end user's perspective from a Linux or BSD distribution given they all run X11 and generally require graphical applications to be built on top of it, but they all do use different subsystem components and libraries.
"If I'm not mistaken, Apple have just made their own Window Manager, of which there are already many to choose from for Linux and they have locked it down where possible to prevent the user from being able to change it."
You are. OS X doesn't even natively use X11 for anything, though an optional X11 server called XQuartz is available. Instead it uses its own display server without all the cruft of X11 being pulled along for the ride. The window manager is built on top of their libraries and is not meant to be replaced, just as Windows' window manager is not meant to be replaced either. You probably can, but I'm not certain on that; it would be an ugly mess.
They have also disabled the standard built in package management system and replaced it with their own library of commercial applications, removing still more choice.
There is no single standard package management system for Linux. Each distribution uses its own. Ubuntu uses Debian's dpkg and apt, as do Debian- and Ubuntu-derivatives; Fedora uses RPM and PackageKit, as do a few others; Arch uses pacman; Gentoo uses portage; etc. There are package management systems available for OS X for other utilities if you so desire, such as MacPorts or Homebrew for example.
Apple use a mixture of FreeBSD user land and GNU utilities on top of the Mach kernel, as I mentioned before, along with several in-house additions. They do use several other products from the free software community such as KHTML in the form of Webkit, but not one of them is the Linux kernel, the one and only thing that makes a Linux distribution a Linux distribution. The terminal will of course feel familiar because it's bash, perhaps the most commonly used shell in Linux, but that's GNU. OS X is in some senses a true Unix, whereas Linux is simply Unix-like.