The answer I got was unclear (slight language barrier). When I mentioned companion, she did start mentioning miles though, so I would err towards thinking that they can't be used for companions.
Couple more questions
1) I'm guessing an Aegean coded TK codeshare flight would not be upgradeable if it's Turkish metal?
2) This doesn't make a difference to me as I have more vouchers than I will use anyway but, out of interest, do you think that IST-ATH-FCO on one ticket is 2 vouchers or 1? Flight numbers are different for each leg but it is a single booking.