That doesn't contain any of the stuff you're calling part of the document. It doesn't contain the history information, it doesn't contain the GFDL, it doesn't contain the license notice, or a copyright notice - it doesn't even contain the title page.
The spirit of the license is that a transparent copy is one that is easily editable. The parts you're saying aren't included are parts which have to be preserved, so there is no need for them to be editable.
While the exact wording may require the history to be editable, you aren't allow to edit it (beyond adding your name, which is done automatically), so that's a pretty pointless bit of pedantry.
It's not pedantry at all. If I want to create a fork of a Wikipedia article, I need a Transparent copy of the entire document. I don't want to go hunting through page after page of history and what links here and all the other stuff I need in order to comply with the license. I want to download a copy of the entire document in a straightforward way, make my edits, add my name to the title page, add a line to the history section, and be done with it. I can't do that with Wikipedia articles, and that's a major material breach of both the word and the spirit of the GFDL.
A possible alternative is to consider the database dumps to be the transparent copy, they aren't as easy to edit, though.
They would also require you to treat the entire database as a single Document. This approach brings us closer to compliance on many parts of the GFDL, but has problems with others. We can go over that approach if you'd like, but you've gotta pick one definition of the Document and stick with it - you can't go back and forth.
No, you could consider the database to be a collection of lots of documents. I don't think the license says the transparent copy has to be available on its own.
I think it's unclear whether or not the WMF is the publisher. But the WMF isn't listed on the title page anyway.
Well, the "title page" says "From Wikipedia, the free encyclopedia". I would say the WMF is the publisher and is working under the name "Wikipedia". The license doesn't define the word "publisher" anywhere, so I think the everyday meaning of the word is what is meant.