I quilt for others, and would never ignore a customers request without discussion. There is very, very little difference for the machine when using poly or cotton. Maybe change foot height if high loft and a MAYBE a tiny tweek of tension. I don't understand why you also didn't get the color thread you wanted. Sounds like she needs to find a different teacher and get a lot more CORRECT information IMHO.
There are a lot of us here on the board, there is even a list of us. I believe it is a sticky on the sale forum. Remember to get things in writing and ask for a prices sheet.