The difference isn't negligible at all. Anyone who has done any multi engine training in a propeller equipped multi engine aircraft understands it immediately, and it's quite visible in the performance of the aircraft. In light twins, it can mean the difference between maintaining altitude and a descent without the ability to maintain altitude. It also make a significant difference in controllability and minimum controllable airspeeds.
A windmilling propeller is responsible for more drag than the equivalent flat plate area of the prop disc. That sounds counterintuitive, but is true. If one doesn't believe the ability of a propeller to cause drag in flight, fly an airplane that can do beta in flight and see what happens. I used to fly a single engine airplane that was designed with a radial engine, but which had been converted to turbines (PZL Dromader), and the installation was rigged such that retarding to idle in flight would slow the aircraft so quickly it would throw one forward in the shoulder harness. One could follow through with the stick briskly until the vertical to prevent a loss of control or stall. It was dramatic.
Windmilling vs. stopped (or feathered) also makes a dramatic difference. Rudder input required in a multi engine prop aircraft is lessened substantially upon feathering (or stoppage of the prop, such as a seizure). The windmilling propeller absorbs considerable energy, driving gearing, accessories, etc, when the engine is no longer driving the propeller.
Prior to a windmilling state, when the engine is imparting energy to the propeller and the propeller is doing work, the combination produces some degree of measurable thrust. In a windmilling state, the propeller isn't receiving torque from the engine any longer, but is still receiving energy from a source, which is the slipstream, and the process works in reverse. Whereas with the engine driving the propeller, that amount of torque and energy went into moving airflow and creating thrust, the slipstream energy now becomes all drag as it drives the prop and that drag is imparted to the prop, shank, driveshaft or crankshaft, and ultimately engine mount, wing and airframe. In effect, the slipstream becomes the engine driving the propeller, and works against the airplane instead of for it.
A stopped propeller experiences a certain amount of flat plate drag area or form drag, but much, much less than a windmilling prop.