I don't think it comes with the book, or box anymore. Certain places online who sell it in the box and with the book, make a big deal of the fact they managed to secure some rare stock. So I'd say it comes in just the plastic blu-ray case now.
I ordered it on Monday and got it today (during which time it's gone up by £9!) and the DVD Set most definitely DOES still come with the book (in a slip case containing the 7 DVDs in a plastic case and the book which matches the DVD case in size and thickness). So basically this is identical to the 40th Anniversary Edition except it's no longer called the 40th Anniversary Edition (because that was 2 years ago)...
Anyone still making their mind up on The Prisoner on Blu-ray, the Network DVD site itself (the company who makes the set) have everything on site with 40% off for one week only. I just bought the Blu-ray set at £23.89... absolute steal. I already own The Network release, but on DVD, and I got the book with that so it doesn't matter the BD set no longer comes with the book as I already have it. I can give the DVD set to a friend now, and keep the book.
They won't stick around at this price, so I'd act quickly if I were thee.