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1. Have you tried using Typst instead of LaTeX? (In my view it has many bugs and deficiencies for good typesetting especially in Indic languages, but a lot of people seem very happy with it as an alternative to LaTeX, so I thought I should suggest it anyway.)
2. If your LaTeX files are autogenerated from MD, why do you care about how "hairy" they look? You need never look at the LaTeX source code anyway, or you could move all this preamble into a separate file and \include it.
3. Ideally IMO for good typesetting, it is best to manually specify what font must be used where, so again if your LaTeX files are autogenerated from MD, then you might as well have an intermediate script that recognizes runs of characters and specifies the fonts for them (e.g. use \textenglish for runs of English text), instead of doing it automatically inside LaTeX itself as you do above (using ucharclasses and \setTransitionsForDevanagari etc). (Using some of my own old answers on TeX StackExchange to refresh my memory :) link, link, link, link.
4. There seem to be several dozen fonts that cover both Devanagari and Latin script, see e.g. here (or more narrowly here) — I think if you're not particular about Noto Sans there may be several alternatives (and I think a Noto Sans that includes both may already be included there? Have you tried downloading recently?)
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I am not able to understand whether we are mixing two isolated concepts, font and Latex etc.Coming to Latex, context etc, I feel that we should give the pain to AI text generators. For example, in Google colab, I asked Gemini - "Write Pythogorean theorem in Devanagari. take a, b, c as ka, kha, ga.
I want to be more specific on the problem you have described and add the following. This problem should not be tried to be given to generative AI. Instead, do the following-1) make minor markup changes (italic, changing size of some types of text etc) using 'regular expression find-replace'.2) convert the resulting text to html (there are many online free tools)3) open it in LibreOffice and do the following-a) convert it into two columnsb) do page numbering3) finally convert into pdf.
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