but one has higher drag than the other (let's say due to appendages to the fuselage).
You're thinking something like this?
I have been doing extensive flight testing on this Caravan, though not for glide speeds, just characteristics, among all the other requirements.
Among many things, I have learned during repeated climb tests at different speeds, that the best rate climb speed has been reduced 11 knots by the drag of the mod. The 20 flap best rate climb flown at the flight manual speed, no longer met the minimum climb requirements for the aircraft's certification basis. Flying climbs at lesser flap settings did meet the requirements, though this was operationally undesirable.
Flying the best rate climb at 80 knots did get me the climb performance required to show compliance to the certification basis. This slower climb speed did, however, introduce other challenges, one of which was demonstrating a land back from an engine failure at 50 feet after takeoff. The slower speed, coupled with the added drag, resulted in a quick deceleration, and a return to the runway that brought helicopter autorotations to mind! It was also required to fly an approach and landing at Vref -5 kt, which meant an approach flown at 70 knots, with the stall warning sounding the whole way down final, and very little let to flare with.
Interestingly, when the survey bird is winched down about 10 feet, the drag is reduced, resulting in a 3 knot increase in speed, all other things being equal. The operational deployment is about 300 feet though, so the drag of the rope has reduced performance again by that point.
Though I did not do direct AoA and glide drag comparisons between the pre mod and post mod aircraft, I'm sure they are not the same....