You absolutely can operate under both 107 and a COA. Remember, just like manned aviation, it's a flight by flight determination of the rules that apply, made by the PIC at the time. You just can't operate a SINGLE FLIGHT under both sets of rules, it's as Licensed Pilot says, one or the other. As far as how you run your program it can be beneficial for both a COA and 107, but many agencies such as Licensed Pilot's, operate extraordinarily well with just a 107 and a night waiver. The complexity of your individual operation should be the determining factor for the statutory rules you operate under (107, COA or Both). As far as an agency needing a COA for the aircraft, that is not correct. You can register your UAS as Part 107 Aircraft and operate without a COA. We have and we do. If your FSDO is telling you that they are incorrect, you can contact John Meehan at the FAA who can verify. I will say 107 is easier to get going under and a night waiver is easy. But for my agency, it gets a little more complex because 80% of my 30 square mile jurisdiction is within the surface area of both a Class D and Class C airport. We have a waiver, with Tower support, pending with the 107 team and a blanket COA still pending. That being said we have conducted flights in the Class D with an Emergency Waiver on several occasions, usually airborne with waiver in hand in 30 minutes. As others have said, I would be more than willing to share our Flight Ops Manual, Policy, Training Materials and Waivers with those who are interested. Great Discussion here.