most of what you want can be automated using calibre- preferences, extra css to convert & tweak each book before loading it to aura. that can strip margins, font-families, widows orphans...
what gave me most trouble was removing all the line height settings so that line spacing slider worded, but the folk on sigil forum came up with a universal regex formula that I run manually on each new-for-reading book
the long paragraph issue is annoying in some books but there's a reader config file hack for that.
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