In the case Lisa is talking about, the author is long dead and his work has already been published. If it is quoted, it must appear as it was printed, and no copyeditor "corrects" his spelling, word usage, etc. (I put the word in quotation marks because what is incorrect to us might have been correct in the author's time.) Now, if you are copyediting an author who is very much alive and who uses unusual spelling, punctuation, grammar, and so forth, what you do is determined by several things. Einsohn talks about these in the first chapter of her book. I'll go over some of her points here.
Well, remember that the copyeditor and author are engaged in a formal relationship. If no such relationship exists, you do not have to comment. Sometimes friends bring us their work to look at; they are hoping that we will be impressed with the work and will praise them. Because we are not in a professional or formal relationship with them, we need not comment if we feel that such comments won't be appreciated or have any beneficial effect. We can instead make the choice to protect the friendship by saying something like "I really don't feel I'm the right person to evaluate this. Maybe it would be better if you asked Mr. or Ms. X?"
In the case of the copyeditor-author relationship, the author has agreed to consider the copyediting in exchange for having his work published. If, in the course of copyediting his work, you question his style, diction, metaphors, etc., it is your right to do so. You are supporting and enforcing the publication standards of your employer.
If the author is offended and/or rejects your copyediting, it is possible that publication of his work will be reconsidered.
It is also possible, as I've said before, that the acquisitions editor will (1) decide that your editing won't be used or (2) enter into a dialogue with the author that will result in a better piece.
P. 3: "Heavier intervention may be needed, for example, when the author does not have native or near-native fluency in English, when the author is a professional or a technical expert writing for a lay audience, or when the author has not been careful in preparing the manuscript." Note that here Einsohn is talking about a manuscript that not only can be made to conform to a certain standard but should be made to conform.
P. 4: "Copyeditors who work for publishers are usually given general instructions about how light or heavy a hand the text is thought to need." Here Einsohn is talking about what the publisher decides should be done to a manuscript. The publisher may decide that the unusual spelling, etc., are an integral part of the book and cannot be separated from the narrative. In that case, the publisher will instruct the copyeditor to edit lightly. For example, if "there" is being rendered as "thar," the copyeditor will need to correct it when it appears otherwise. In the passage Lisa quotes, "linendrapery" is used, but if the word appears as "linen drapery" elsewhere, Lisa might correct it, noting in the margin that the correction has been made and referring to the previous instance so that there's no question why she did what she did.
P. 4: "In addition to having a good eye and ear for language, copyeditors must develop a sixth sense about how much effort, and what kind of effort, to put into each project that crosses their desk." This sense is called editorial judgment, and the copyeditor acquires it only after working for publishers and with authors for a while.
P. 5: On this page, Einsohn lists such elements of mechanical editing as spelling, hyphenation, capitalization, punctuation, treatment of numbers and numerals, treatment of quotations, use of abbreviations and acronyms, and use of italics and bold type. When I said a couple of times in class that consistency of treatment equals style, I was referring to these elements. When the copyeditor makes the manuscript internally consistent, these are the things that he or she focuses on.
P. 5: "The mistake most frequently made by novice copyeditors is to rewrite portions of a text (for better or for worse, depending on the copyeditor's writing skills) and to ignore such 'minor details' as capitalization, punctuation, and hyphenation. Wrong! Whatever else you are asked to do, you are expected to repair any mechanical inconsistencies in the manuscript." Note that here the temptation for beginning copyeditors is to make the manuscript with non-standard spelling, etc., conform to what they have been taught. Most of the time, of course, you will be expected to do just that. Every once in a while, however, the publisher will not want you to do that. When you are given a manuscript that should be treated in a special way, it should be made clear to you what is expected.
P. 7–9: "Ideally, copyeditors set right whatever is incorrect, unidiomatic [not natural to a native speaker], confusing, ambiguous, or inappropriate without attempting to impose their stylistic preferences or prejudices on the author.…[T]he 'correct' usage choice may vary from manuscript to manuscript, depending on the publisher's house style, the conventions in the author's field, and the expectations of the intended audience.…Copyeditors are expected to correct (or ask the author to correct) locutions [style of speech] that are likely to confuse, distract, or disturb readers, but copyeditors are not hired for the purpose of imposing their own taste and sense of style on the author. Thus when reading a manuscript, the copyeditor must ask, 'Is this sentence acceptable as the author has written it?'"