The CSS for the first set of header selectors can have both margin-top and margin-bottom, and then the second set of selectors isn't needed.
The Story of the Flower Kingdom in chapter 10 is just the poem, so that we need either the section or the blockquote, but not both. I don't think the blockquote is applicable, since he's not quoting someone else, so the poem semantic should therefore go on the section and eliminate the blockquote. Just the blockquote—the rest of the formatting, with the p and spans, stays the same.
You appear to be on an older version of the tools. Go ahead and update them, and then re-run lint; you will need to update the ignore codes to match the new ones. (The t-042 code was split into various y-XXX codes a while ago.)
Typogrify makes a change that should be accepted.
CSS is needed for the Latin blockquote; see SEMoS 8.2.9.6.
Likewise, CSS is needed so the "Jurgen" is not italicized in the introduction quote. (You've surrounded it with <b>, but it's not small-capped in the scans.)
Commit e987609 is changing the text, so should be an Editorial commit.
On the other hand, commit e122e05 is not changing the text, just as your other "fixing transcription" commits, so should not be editorial.
And, since we're changing commit messages, 0b48475 has the "git commit -am" in with the message.
The song in the prologue is missing the beginning quotes for each stanza (and the quotes should match the scans).
Also, the last line of that song is not italicized as it is in the scans.
I think the missing punctuation in the letter in the prologue is intentional, just as the misspelled Amen (and missing comma before it), so they should probably be removed. (It will require ignore entries, I'm sure.)
The "Fable of the Foolish Prince" in the prologue is a story (everything after the title in section -2 is in quotes), and should thus be formatted as the rest of the stories, i.e. as its own section, with the title as header.
The story sections should have ids consistent with the others, i.e. prologue-2-1, not the name of the story.
I'm also not sure about the use of z3998:subsection; they would not seem to qualify for the definition (they're not "major subdivisions," since they're only part of a part). But, I don't know what else might qualify, either. (It may be we leave it off entirely). I'll ask Alex on-list.
The colon in "But now: I recognize…" in ch. 7.7 is not present in the scans.
As the clause is standalone, I believe the exclamation on "Depardieux, messire!" should be within the italics.
Several tagged word/phrases are in M-W, so should not be tagged: e.g. fin de siècle, au revoir, ignis fatuus, etc. Other than long quotes, any word/phrase needs to be checked against M-W; see SEMoS 8.2.9.4.
Since it's prefaced with "some of the new books," and there are Mr. Dooley books, even if that isn't the exact title, I think we should go with the scans and tag "Mr. Dooley" as a book in ch. 7.4.
Only book-length poem names are italicized; short poems are quoted; see SEMoS 8.2.11. They can still have the poem semantic (although I can only find mention of “Me und Gott” as a song), but they're quoted.
The blockquote in chapter 9 is a letter ("…wrote Uncle George"), so should be tagged as such.
The "For she is to each man…" paragraph in ch. 11 is not indented, so should have the "continued" class. And since it's not starting a paragraph, which means the quote isn't either, the extra quotes aren't needed. (That differentiates it from the earlier verse in the same chapter; there the quote is a separate paragraph, and so needs its own quotes.) An argument could be made, I suppose, that it should be single-quoted, but since the scans don't, and we're not in the business of re-editing the book, I think we leave it as is.
The "allways" in Avis' letter in ch. 28 is intentional (see the second para of the section), so the commit to correct it should be reverted.