I'll tackle two other concerns. If you use bentonite as a seal, that seal will be near the surface, to several inches below the surface. Tree roots won't bother the seal. To be safe, plant the trees far enough away from the pond to be sure the drip line never encroaches the area where your bentonite seal starts.
Second, you asked about a rock spillway or pipe.
If you intend to re-use the water, pipe it downhill, where you want to use it again. Rock spillways increase surface area of water contact with air, increasing evaporation. It may be a minimal impact, but when water is a precious commodity, every gallon counts, especially if it goes into a garden or the tummy of an animal.
