@Agame
It seems that we don't agree in fundamentals about markup. That's OK. No offense.
But we will not find a consensus in this area, I suppose.
We are asking very different questions, from a very different point of view.
You ask: Why isn't that extra class OK?
I ask: Why do you need an extra class?
About "plain text":
That does not fit my needs.
I need and want markup in books.
Headers.
Emphasized text.
Ordered lists.
Footnotes (Links).
Blockquotes.
Images.
Data tables.
...
Your post-conversion plugin:
I'm not sure, if I could use it, when the source isn't a markdown format.
Do you have please a complex example of "before" and "after" (the conversion).
I'm interested in what your plugin does