From my perspective, as someone now dealing with acropora eating flatworms and ick, both in a single quarantine tank (which will now need to be broken out into two tanks so I can treat the ich), your choices are two quarantine systems, one for fish and one for coral and everything else bought 'wet' to be put in your system (snails, inverts, etc.), or buy from a very reputable on-line source such as Divers Den and still take a small chance of something bad happening. To be extra safe, you can buy from someplace like Divers Den and then quarantine.
72 days seems long but, everything else being equal, longer is better than shorter. I recently bought a yellow tang locally that I quarantined for 6 weeks and then put in my display without incident. Personally, I'm on the verge of giving up buying anything live from my two LFSs. For me, at this point, the added peace of mind is worth the extra cost of Divers Den.
In terms of processes, people do anything from just watching stuff in quarantine to actively treating even in the absence of no signs of disease. I treat with Prazipro automatically and observe the fish for signs of illness that may need to be treated with something else. Corals get dipped in Coral RX with close attention paid to what comes off the corals (this is how I discovered my AEFWs that came off some acros bought at a frag swap last weekend).
As much of a pain in the *&% it is to have AEFW and ich right now, I am very thankful I'm dealing with both in quarantine rather than in my display tank.
Matt