Is there a way to simplify the EPUB output in the latest updates?

With the updates adding "more control over CSS," I find that there's a CSS file generated for every document in the book.
It used to be that there was one style.css file for the entire EPUB, and that made it easy for me to change <span class="CharOverride-N">...</span> to <em>...</em> when streamlining the eBook.
But now, in one document, <span class="CharOverride-1">...</span> is bold, in another document the same class means italic. This change has turned a 30 second process into 60 minutes, since I have to check each document one at a time to do the correct replacement.
Is there a way to revert to the previous behavior? Or to make the output consistent so that the overrides are the same in all files?
Or, even better ... if a span of text is marked as [Font Family] Italic, why can't InDesign just output <em>...</em> with no spans and no CharOverride styles at all?

This is a good tip.
When I first encountered this new behavior, I did add a new character style called "Italic" and one called "Bold." I set each to the corresponding tags of em and strong. Aside from the oddity of <em class="Italic"> and <strong class="Bold"> this does seem to present a significant improvement.
However, the character styles are obviously not applied when I place a story that has bold and italic in it or when I change to italics on the fly (using keyboard shortcuts). Am I correct in understanding that I need to go back through all documents to replace italics with "Character Style: Italic" and bold with "Character Style: Bold" throughout the book?
Also, I'm good with changing this process for books going forward, but I'm wondering what the simplest way to update past books will be. (They only change in response to errata, and that will happen semiannually at most.)

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