The fact that they require PDF is actually due to their own stupidity.
They force you to convert a perfectly good DOCX or EPUB into the
incredibly lossy PDF format, only so they can go OCR (

) the PDF and turn it back into an EPUB for digital publication.
PDF is a weapon of last resort! Only use it if you literally have no other choice!
It is not a matter of "there are no good/reliable conversion tools". it is a matter of "a PDF by definition has all that information stripped out. No conversion tool can summon the lost bits from the abyss of the original DOCX-to-PDF conversion."
Ligatures are by comparison small potatoes.
IIRC @Hitch has a number of instrumental screams about the PDF workflow

she works in the biz.