Hi,
I’m really curious about some of Scrivener’s auto-change settings available during compile, such as changing italics to underline and vice versa, or converting em dashes to double hyphens.
I’d be interested to learn why these conversions might sometimes be necessary? Why would a writer use italics in a manuscript, but need to convert this to underlined text at compile?
Is it something to do with eventual print requirements, or ebook formatting?
House styles vary. And who knows what an author might want to do. I remember I once read a philosophy text in which the author quoted from other texts, and sometimes wanted to add his own emphasis to what the original author had emphasised. This resulted in phrases that (if I remember correctly) were not only in italic, but some words and phrases had spaces between each letter. It was quite difficult to read – in all sorts of ways.
I am currently fond of writing drafts in a typewriter font that doesn’t support italics.
So in the draft I use underlines, and during compile convert the underlines to italics and my fun font to Courier. 
Like much of Scrivener, many of the Compile settings exist because specific publishing niches have specific requirements.
(Arguably, that’s why the Compile command itself exists.)
They are there because one day you might see a guideline sheet that requires Courier 12, double-spaced, with underlines, but you’d rather listen to Vogon poetry than look at Courier 12 for 100,000 words.
Katherine
Some of these are historical to an extent. It used to be that the manuscript submission guidelines of many publishers required the use of underlines for emphasis instead of italics, because underlines are more obvious than italics regardless of the font used. And they also required double hyphens to indicate a long dash, to make it easier to differentiate them from regular hyphens. Many of these conventions originated from typewritten manuscripts, before word processing, but stayed in place for many years after the word processor become ubiquitous - this was still the standard advice for manuscript submission back when Scrivener was first launched, twelve years ago. So, these features allow users to write using italics and long dashes, but to have them converted to “standard manuscript format” during Compile. I don’t think many publishers have such requirements these days, but the features remain just in case.