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It will probably take a generation to reach consensus, although I agree that the consensus will eventually favor "website." Most people will stick with the way they learned it when they first got onto the Web (as evidenced by my continued use of a capitalized W on "Web" and my stubborn refusal to write "email" instead of "e-mail").
But eventually, we Internet dinosaurs will die out and be replaced by younger, more nimble creatures who won't be slowed by spaces or hyphens in terms that are, to them, common terms of everyday life instead of terms that were coined to describe what was, to us, the new and emerging world of the Internet.
Sorry to question and argue, but your statement is true only if you are writing for publications that use the AP Style Guide as their standard. There are numerous authoritative style guides used by large segments of the writing profession out there - the Chicago Manual of Style, and the Microsoft Style Guide, to name just two.
In matters of how words (like Web site/web-site/website) that are in flux are treated, these equally authoritative style guides are usually split, with the AP style guide tending to perpetuate older forms of spelling long after common usage has adopted newer ones.
The style guide you use depends on the style guide that the people you are writing for have chosen to adopt (or the style guide that someone back when you were learning your writing profession told you was the official one to use for their class or business).
No style guide, however, serves as the "official" authority that GOVERNS how the English language MUST be used. Each of them is at best a document of the usage and speling choices its editors have made, at that point in time, for the sake of having all writers for their organization be consistent with each other.
In time and through common usage, dictionary makers change these split up terms to either a term on their own 'web site' with a specific definition or hyphenate it to 'web-site'. This stage is sometimes missed and they may go straight to:
Website. Which would be how this word will eventually be spelt. It is such a common word nowadays that any dictionaries or references that state it should be 'web-site' or 'web site' will eventually update to 'website'.
Same with 'E Mail', 'e-mail' or 'email'.
How you use it in the early stages in more a matter of choice.
And don't forget that there may be one way to spell the same word:
Look in an English dictionary for (not an American - they are often more strict):
Dispatch and Despatch - both spellings are perfectly acceptable and the meaning is identical.
It has evolved as do many other words, beginning with web site, gradually gaining great usage and being promoted to hyphenated status, and then eventually becoming generally recognized as a single word. Similar to E mail to e-mail, to email. Newspaper is great example.