Perhaps one of these articles will help:

5 Reasons for Unexpected Overset Text

or

Tips for Fixing Overset Text

Well, it depends on what you mean by “accurately” and “non-destructive.”
To flatten and simulate overprint, you could set Compatibility to Acrobat 4 and then turn on “Simulate Overprint” in the Output section.

No, I don’t know of any way to tell if they’ve been used. They’re called “Styles” but they’re not really styles… that is, they’re not linked to TOCs in the doc, so changing them doesn’t change the document. They’re more like “Print or PDF Presets”

I’d just delete ’em. :-)