Best glide speed refers to best lift to drag ratio. Although there is a best lift to drag speed with any configuration, it will be decreasing the more you increase parasite drag on the aircraft (adding flaps or gear). So when experiencing an engine failure when the aircraft is clean and adding flaps the difference between your actual speed and best L/D = glide speed gets bigger ( in most cases unless you fly the aircraft close to stall speed),i.e. you waste lots of energy and thus gliding distance. Furtheron the L/D ratio itself will greatly decrease as soon as you change from clean configuration. So even when maintaining best glide speed for flaps (and gear) extended your descend gradient will always be steeper than clean. A windmilling prop will make a big tradeoff on gliding distance, so feathering the prop ( if possible) is crucial.