Duffel bags are often used as personal items, even if they are more of a carry on size than a personal item size. It’s a common way carry-on-only travelers try to maximize what they can bring (if you’re not flying a LCC). As we know, it is customary to ask that overhead space be used for the primary carry on and that personal items be stowed underneath the seat in front of you to ensure overhead space is used for as many carry ons as possible.

My guess, based on your statement that the FA didn’t sound like she was trying to be be abrasive but was genuinely serious in thinking this was the right thing to ask you to do, was that she maybe wasn’t computing that the duffel bag WAS your primary carry on, and that the backpack was your personal item.

I would’ve just made that designation very clear, using those specific terms (primary carry on, personal item), and would’ve asked why you were not being allowed to put one carry on above and one personal item at your feet as is typical. If she still wasn’t understanding the logic, I too would very politely ask to speak with a lead under the guise of needing clarification as to why you weren’t entitled to use overhead space for your carry on while safety tucking your personal item under the seat in front of you.