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This is actually a misconception.

IE is not a true part of the Windows.

IE resides entirely within user space and uses only standard MSDN documented APIs.
IE gives the impression of being embedded into Windows because it is seamlessly integrated with many other components like Explorer and the help systems.

Media Player has been integrated in the same manner. both IE and MP can be removed but give the impression of being non-removable because there is no functional equivalent to replace them so alternative solutions fall short....
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Hi Catch,
I wonder if you could clarify a bit the difference between "seemlessly integrated" and "embedded"? I'm not a computer/software person by training (except through self-study here and elsewhere). But it seems to me that the main point is removal of IE causes loss of functionality as you have said. Is the following a fair statement? I could say that the pistons in my engine were either "embedded" or "seamlessly integrated," but either way, if the pistons are removed the engine will not work as designed.

Getting back to software, I can install Opera and then uninstall it from Windows without breaking any functionality.

I'm not seeing the distinction you're making.