The W3C also says:
"DOCTYPEs are required for legacy reasons. When omitted, browsers tend to use a different rendering mode that is incompatible with some specifications. Including the DOCTYPE in a document ensures that the browser makes a best-effort attempt at following the relevant specifications."
Since no ebook reading software I know of requires or uses a DOCTYPE for anything at all, I'd go with the WHATWG on this one.
Not to mention that the DOCTYPE the W3C reuires is <!DOCTYPE html> not the XHTML doctypes.
In any case, I am done trying to convince people, IMO DOCTYPEs are obsolete. You are welcome to reach that conclusion at your own pace