There are a couple of existing threads worth looking at, as much of this has been discussed already:
- One click compile
- Compile: disable replace (note, I posted a Keyboard Maestro macro to this one, for Mac users. I believe there may be an AutoHotKey script for Windows users floating around as well, but I don’t have the URL in my notes).
But as an aside on ePub, when I’m doing fine tweaks like that I do them in an ePub editor, such as Sigil. Such changes appear in real time in the preview pane, and so I can very quickly get a look I like, and then take what I changed back to Scrivener, doing one compile to confirm it worked the way I expected.
This is the approach I take for almost everything. I compile once, and then revise and tweak on the intermediary or final file, making the change in Scrivener as I go. I typically at most only compile two or three times for what would probably be dozens of compiles if I didn’t work that way. Why spend accumulated hours waiting for compile when most editing environments provide real-time feedback? And if you’re reducing how often you compile, then things like confirming overwrite become far less of a point of friction.
For PDF I can’t really help you there, except to say you’ll get a better result by creating PDFs from other programs anyway (where all of the above applies), so that’s a bit of an awkward one to begin with.