Thank you Kovid, that's exactly what I was looking for. Clearly I didn't look through the tweaks as thoroughly as I thought I had.
For future reference, the exact tweak is called "Control formatting of title and series when used in templates". After setting it to 'strictly_alphabetic' instead of 'library_order', all books are now saved as I wanted:
"Machen, Arthur/The Three Impostors 02 - The Novel of the White Powder"
Unfortunately the Send PDF via Email issue remains. I'll look into it further to see if there's something else I'm missing.