I could be wrong on this, but I believe you can only utilize one FF program per reservation… for example, I’m Delta GM but in order to have my ST Elite+ recognized when I fly on an Air France booking I cannot have my Flying Blue account attached at all or it will override my Delta status.

Might be less that DL reps didn’t know about Elite+ but rather were confused about trying to double dip when you have the SkyMiles attached to the booking already.