Taking your very helpful suggestions and information into account, I decided to produce a separate tool (ReLaTeX) that "re-templates" Sphinx latex output into any latex file you want to use as a template. That is, it extracts the relevant content from Sphinx's latex output, and uses a standard templating system (Jinja2) to "inject" that content back into whatever latex file you want to use as a template. This has worked well for me on a number of papers for different journals, and hopefully could be useful to other Sphinx users. It has the added advantage of being useful for "re-templating" *any* latex input, not just latex produced by Sphinx. I'll post details about the ReLaTeX release separately so that other Sphinx users can see them, but I wanted to thank you for your very helpful feedback.
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