Here's one last issue I was having with the files (once these two problems are sorted I'll be able to successfully render in PDF

)
If I take this file for instance, which is supposed to show Greek characters, it's instead just displaying plain UTF-8. I wonder if I can somehow tell Calibre to display it like it says to do inside (what was originally) the XML file...
Here is an example file to illustrate what I mean:
https://raw.githubusercontent.com/Pe...rseus-eng1.xml