Well, with websites everyhing is loaded over the internet, and you can take advantage of server-side processing to feed different user-agents custom resources... oh, and [if IE] comments!
And you can always update as you fine-tune the results.
So websites are a work-in-progress, and testable via software... whereas ebooks are
offline websites, and there are what, dozens of different
hardware devices you need to test?
In terms of actual specs conformance, I don't know how different they are -- and I claim no expertise -- but I can see why ebooks should cause a lot more grief simply due to the inherent decentralization and non-specificity of design.