Hedgedrew,
I would not quarantine in tank if I were you. Getting something like meds into your system could have further consequences as would the possibility of letting parasites into the tank in the first place. If this was a fish only artificial reef then you might be able to pull this off, but in a future reef tank with calcium carbonate rock which is porous and not chemically inert I would not quarantine in tank.
If you only use prazi and hypo then it could work, but if you find yourself going with other meds because they don't work for whatever reason then you will open up another set of issues. You can always quarantine in a stock tank system. Cheap and easy to set up and tear down as needed. 300 gallon stock tanks work for most species and multiples can be plumbed together if necessary. Can't view horizontally but still can work. They make up to 1000 gallon stock tanks that are 36 inches deep.
Best is still a traditional quarantine system. You can't get away with the groups in small tanks so you either need big quarantine tanks or lots of smaller tanks plumbed together. In the public world we used a combination of these systems depending on species considerations.