The licensing of the layout is of course separate from the licensing of the text. The use of Jekyll too is without effect because Jekyll isn't distributed together with the work, nor the licensing of the GitHub SaaS code for hosting. With the PDF, physical print copies and an e-book (the latter for the reason of font embedding) however, it's different, because I would assume that these are a "combined work" where you are using + distributing the layout and font under their licenses, and you can't separate or strip out the parts that are licensed under X11, so a user indeed still receives the text part under CC0, can share and modify it under the conditions of CC0, if the layout and font is removed (typing the text off, OCR, removing the layout parts from the EPUB for subsequent redistribution, which renders the included layout a little bit pointless but anyway), but for the files we provide and may subsequently distributed/modified by users and third parties, these do include the layout and font and therefore practically speaking have to satisfy both the requirements of CC0 as well as X11, because in these cases, the two parts of the work are not distributed separately (so for any practical use case, an end user might not encounter the Jekyll or GitHub dependencies with their licenses, but would those of the layout and font). On the license waiver page for the text and in the metadata of an EPUB, it would/should need to say that layout + font is copyrighted + licensed under X11 by its contributors, together with text + images under CC0, and an end user has to agree to both, for the work as presented. Note that in print, I think the current status is that the use of a font on the page is not copyrightable, but a layout may (especially as the people who did the Tufte layout claim copyright in order to establish X11 licensing, which may target the "expression" of their CSS code, but almost certainly is intended to expand to the layout as well, where no reliable assumptions can be made what would be considered an infringement and if the creators/designers would enforce their copyright, just in any case, their work isn't under CC0, and CC0 and X11 aren't the same, therefore it's another legal complication caused by stupid print-era copyright regulation incompatible with the digital age and inadequate "open" licensing practices, for which solutions may or may not exist). Same would apply for the Apache license for the layout for LaTeX, if the web X11 variant doesn't get ported to LaTeX. It could be that the X11 is vague/ignorant enough that the required license notification could be included somewhere in an e-book, but not displayed, which might not be entirely "safe" to do it this way, but wouldn't work for printed books and PDFs for the layout (minus font embedding in PDF/EPUB). Anyway, this isn't legal advice, just my current understanding of how the copyright law works and what the authors/creators stated as their demands/intentions. I think I'm personally much affected because I'm not a handbook content contributor. Contributors might not mind that their CC0 text becomes part of packages that also have a X11 requirement, and there can still be variants without the Tufte layout. Just for uploading to distributors and printing, as well as the end user + third parties, they wouldn't be allowed to remove the X11 license notification for redistribution which includes Tufte layout + font, which they are permitted for earlier handbook versions and continue to be for the CC0 text up to copyfraud/re-licensing and proprietary use, which the X11 would prevent now for these combined works, and if I'm not mistaken, it was an important point and legal feature to specifically allow proprietary use and copyfraud (in the hope to encourage wider spread). The Tufte contributors with their work obviously are not in favor of this for their part.
Technically, I haven't looked into the whole Tufte thing yet, don't remember if fonts get extracted and packaged to EPUB if referenced in CSS (if that's what the Tufte CSS is doing), which all may come easy/cheap or maybe not. I did see that they rely on some additional markup, and most concerning, that it's partially HTML5. EPUB3 was (still is?) at the forefront of HTML5 and relies on it in some sense, included it even before the spec became more static (but now these Web people don't even want to have specs and versions any more), but then EPUBs are (and reasonably so) expected to be valid (plus I'm not going to do anything around broken XML HTML5, and don't want to invest much into proper/full XHTML5 or XHTML5 Polyglot, especially with W3C, WHATWG, browser vendors actively sabotaging and degrading Web technology), so let's see if it works out for the Tufte layout, or if it enters into a dirty, stupid mess. For Markdown, I don't know, arrived at the concept that it's just a textual interface for writing (not a very good one as its supposed simplicity easily breaks down where people want to do all kinds of more complex expressions in it, which requires non-intuitive syntax) where the process also gets confused with markup/layouting/typesetting/semantics, so writing + semantic markup could be separate concerns or maybe more importantly, the Markdown plain-text syntax writing/markup interface shouldn't be confused with a proper data format that actually comes with real semantics and stuff, so maybe there could be a conversion from Markdown to ideally (namespace-mixed?) XML or something, maybe with an extra parser/pass that handles our own "extensions" (not to the Markdown "format", but our variant of Markdown as a writing interface/convention), like Mediawiki with the Wikitext writing interface (targeting HTML output, still confused with a data format but anyway) uses server-side template plugins/parsers to do all kinds of special, custom processing that's not necessarily supported elsewhere or standardized beyond their own domain. If we would go down that route, OK, the question might be asked of why to continue to bother with Markdown to begin with, or if something else could be used, some other textual writing interface/convention, or maybe (as it could be, but rarely is) one or several ordinary or specialized GUI(s). In any case, I currently don't have a Markdown parser of my own (somebody said it's difficult to parse, maybe because of strange and exceptional random nested symbols that need to be taken care of), and only using Pandoc because you guys had that on board already, previously. Isn't YAML headers in there already too? And XML (HTML fragments) is in the "Markdown" source files just as well (barely retaining that during the use of Pandoc by going Markdown to HTML first and then to LaTeX or whatever, in the hope that XML never conflicts with Markdown special characters). As said, don't know about how I would go about this technically, not overly concerned yet, in contrast to the legal questions because there's always the risk that no amount of effort might be able to resolve issues caused in the latter realm.