Removal of the byte order markByte order marks in UTF-8 can be removed by a properly configured editor. Or the literate feature can also be used to remove them, see above and here:literate={^^ef^^bb^^bf{}0} See Ulrike Fischer's answer to xport's question "How to suppress...
If you look around you will find many tools that advertise that they can produce nice accessible PDFs, but you will not find tools that advertise that they are particularly good at using accessible PDFs. You do not find much documentation how the different options interact or can be configur...