Thank you for the answers! I add my own since I found it on the todonotes package author's blog page:
http://midtiby.blogspot.com/2008/05/updated-todonotes-package.html?showComment=1215360900000#c7770492295748791763
Your problem with the "Marinpar in page x moved" is probably caused by placing several todonotes on one page. If two todonotes (they are in fact marginnotes) are goin to overlap, latex will try to move the todonotes up and down on the page to avoid the overlap. To let the user know that the marginpars have been moved, the warning is issued.
In fact, just deactivating the todonotes packages makes the warning go away. This is fine since those notes are only useful for the draft version.
Well I'm pretty sure Edward Tufte justifies the use of side notes in his work, but I honestly can't tell you which of his books you should consult to find the answer because I have not read yet.
About the justification of the side notes, as you should know, the classicthesis class is a homage of the book The elements of typographic style by Robert Bringhurst, so Andrè Miede tries to emulate the look of the book with the class. Hence also use side notes, for which in the book Bringhurst himself says the following:
If notes are used for subordinate details, it is right that they be set in a smaller size than the main text. But the academic habit of relegating notes to the foot of the page or the end of the book is a mirror of Victoria social and domestic practice, in which the kitchen was kept out of sight and the servants were kept below stairs. If the notes are permitted to move around in the margins (as they were in Renaissance books) they can be present where needed and at the same time enrich the life of the page.
Footnotes are the very emblem of fussiness, but they have their uses. If there are short and infrequent, they can be made economical of space, easy to find when wanted and, when not wanted, easy to ignore. Long footnotes are inevitably a distraction: tedious to read and wearying to look at. Footnotes that extend to a second page (as some long footnotes are bound to do) are an abject failure of design.
Endnotes can be just as economical of space, less trouble to design and less expensive to set, and they can comfortably run to any length. They also leave the text page clean except for a peppering of superscripts. They do, however, require the serious reader to use two bookmarks and to read with both hands as well as both eyes, swapping back and forth between the popular and the persnickety parts of the text.
Sidenotes give more life and variety to the page and are the easiest of all to find and read. If carefully designed, they need not enlarge either the page or the cost of printing it.
In my opinion, the margin notes are usually functional, showing you the information at the right time and not too distracting to reading, at least not as much as a footnote. Here I disagree with percusse and Brent.Longborough. Given the fact that a note is just that, a brief mention is outside the idea developed in the main text but is worth mentioning. However sometimes the notes give rise to a simultaneous development of divergent ideas and main text, that in my view is not just a failure of design but a lack of clarity from the author also.
While the use of long notes is legitimate, when they are so, I think it is more convenient to use footnotes, as though distracted momentarily reading the main text, they are much less distracting than endnotes, I hate them. It is horrible to be reading a good text and then having to flip through the end of the book for the note or notes to which reference is made. Often you have to re-read the main text to resume the thread of the idea. If the volume is very large and unwieldy they are hell.
Formerly many printers and typesetters loved endnotes, as they were much easier to typeset than margin notes or foot notes. But in the twenty-first century with all the technology we have, the endnotes lack that old justification. They are more synonymous with laziness by the publisher or the author (who is often its own typographer and designer), and disrespectful for the reader.
Best Answer
You have adjusted your page margins, but haven't adjusted the marginpar dimensions to match. I suggest adding parameters to your call of the
geometrypackage:This will also allow you, if you need, to see the content without re-specifying alignments.