I continue with the subject of charging non-editable text subject.
Another way is when you get the source file do a mental estimation of how much time it would take for you to do the extra job related to this file and then ask for an additional fees of say 15-30% extra per page or per word.
Some clients accept it, some refuse to give extra charge. It depends how you were able to educate the client about the complexity of the job. Yes, very often it is required educate the clients.
If still he does not agree then you can say ok, if formatting is easy then I shall provide un-formatted text and you take care of formatting at your end.