This is an excellent observation. The airplane gains altitude as the flaps are initially deployed because lift is momentarily increased. Total lift is increased as the flaps are going down, because speed is still relatively high and the AOA is often not being decreased fast enough. Then, when equilibrium is again reached, the nose of the airplane is usually lower than before flap extension, even if a constant altitude is maintained.

Normally much more down-elevator is required to keep from ballooning AS flaps are being extended, than in equilibrium with flaps extended. Therefore, I would use the amount of mix that gives me the desired glide trim in equilibrium. Making sure speed is already low before flap extension, and being ready with elevator correction minimizes ballooning when flaps are being extended.