The following are in my experience and aimed to help you succeed. Please do not take offense. Anything you don't agree with simply chalk up as crazy forum myth but as stated, this is MY experience with some of the animals on your stock list. You don't have to agree with them but I am not trying to start a debate.
24 fish seems like a lot for this size tank
It is quite a lot and this is just a preliminary stocking list. Also keep in mind this is a cylinder. Much different than the typical box. And it is a true 125 gallons. Unlike most tanks that are sold on model rating rather than true volume. The anthias may be nixed. And maybe the emperor. It's also possible to do just one bannerfish, but I thought 3 schooling around the tank would be a great effect. Also keep in mind, this isn't and never will be a hard coral reef. So the softer corals will likely appreciate the slightly dirtier water. Of course all of the fish won't be added at once, so I'll try to monitor everything as I visit the tank.
I believe the angels will keep your coral irritated at best.
This I'm aware of and therefore am choosing mostly noxious soft corals and only those that grow and reproduce rapidly, with the exception of one torch and a few mixed zoa colonies.
Hippos commonly eat zoanthids.
Perhaps. There is no such thing as 100% reef safe. I've had a yellow tang devour a maxima clam. Luck of the draw, but a hippo, in my experience hasn't touched a coral. But again, with any animal there is no guarantee and zoanthids are not typical of a hippo tangs diet.
The chromis will eventually kill each other.
This is a possibility. However, not a certainty. For every post we see about them dwindling down to one, there are a number of post that report just the opposite.
The puffer will eat your inverts.
Indeed, I expect that hermits and snails will have to be replenished periodically.
The shrimp will need to be purchased as mated pairs or they will kill each other although coexist individually.
I have not had this happen in my experience, but they will likely be introduced together. Whether mated or not.
Emeralds commonly eat zoanthids.
It's possible, I refer back to my yellow tang and clam incident.
Scarlet hermits will eventually kill all your snails
Scarlets are usually the more docile compared to other species. Again, in my experience, I haven't found this to be 100% true. However, I added a number of empty shells to my system to allow my hermits an easy way to upgrade their home. But I'd expect some of the clean up crew to be preyed upon. The wrasse and valentini would be more of a concern than the hermits.
Brittle stars can get quite large and become fish eaters
It's my understanding brittle stars typically don't get as large as serpent stars and rarely prey on healthy fish. Furthermore, most of the fish in my stock list would not be an easy meal. Especially since I expect most of the fish to dwell high up the rock work given the 36" height of this tank.
Purchasing juvenile large fish with the intent to remove as the fish out grows the provided habitat should be avoided.
If this were a home aquarium, I would agree with you. However this is a commercial system with a commercial maintenance company. I just have the pleasure of building it because it's family. With the exception of the emperor angel, I believe all of the other fish could live full and complete lives in a 125 gallon cylinder. Remember the unique nature of this tank is there are no walls. They can swim in circles till their hearts content.