Why do we still need to submit horrible looking manuscripts (double spacing, figs separately) to journals when we build them in LaTeX? 

I actually have no idea what you are talking about you've lost me.
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I write in Rmarkdown. That gets converted, using pandoc, into a PDF, through XeLaTeX, which generates figures separately
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That's great for you but I don't think this is relevant to me at all.
End of conversation
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