Hi, George!
I think I understand your issue now. I tried out the new Moodle offline grading system you are takling about and I haven't had any problems with commas or double-quotes. (Haven't tried ellipses.) I'm generating the CSV file with MS Excel, which appears to be "protecting" the commas by enclosing the entire field in double-quotes, and doubling the double-quotes in the actual text. (E.g. ""This is a quote."") Can you get your automated algorithms to do that? That should eliminate the need for tab delimiters.
Your request for permanent ID's seems very reasonable --- have you put in a Moodle Tracker entry for it? I would vote for it.
----Josh
ETA: I can send you an example of a CSV with "protected" characters if that would be helpful.