I really doubt you'll ever find a rule for magic like the type used in this story hook. There has to be more magic in the world than what the PCs can do, so some things have to fall outside the explained rules. Lets face it, most magic for PCs is combat magic, it's quick, easy, and portable. For NPCs and enemies GMs can add magic that is not portable, not cheap, not quick, and therefore not in the rules for PCs, but it's legal cause the GM said so.
I haven't read the story, but I've always used the combat magic vs ritual magic for magic I don't want PCs doing. It sounds like this guy has a set location and has magic that only works in the location. Explaining it beyond that is fluff. A set of magic circles around each cage, an item linked to the circle magic that only works within the runes set into the building walls. It's only available in a set location, add expensive and lengthy rituals to maintain the pattern of runes and it becomes a simple, easy to explain magic, that is less than desirable for PCs to use or copy.
As for the question of the practical side for keeping a black dragon, a golem and whatever else... Given that it's this AP, stasis chambers for holding powerful magical creatures without issue comes to mind. If you want to go with the money is no object and location specific explanation again, dominate monster (control construct) magic set into each cage could control what a prisoner can and cannot do while in the cell. If you get argued that you can't use the permanency spell for such magic and don't want to use the expensive ritually refreshed rune explanation, then change it to magic items. If you upgrade to artifact level items you can do whatever you want almost. Ancient master/slave binding artifacts, slaves get collars and master gets a ring, dominates slave and allows master to use a slave's ability. Artifact destruction conditions don't have to be hard to meet, so add destruction for the master ring as removal from the location it was made to work in, and it becomes useless to the PCs. If the PCs want to do stuff like this, it should be reserved for when they can create magical artifacts themselves.