for the permanent quarantine set up was that barebottom with live rock? if not i see no difference from the permanent and temp quarentine set up
The difference between both is not due to hardware or rocks, i dont recommend rocks in QT at all under any reasons.
Difference in 2 is of the method used.
Permanent QT is a cycled tank just like you main tank that does not require means to remove ammonia somehow while temp QT is not cycled and require a person to remove ammonia with use of chemicals or water changes etc.
Permanent QT requires time to establish and in some cases reefers may not have time to wait 2- weeks for tank to cycle such people can setup a tank and move/medicate fish right away in a Temp QT keeping ammonia at bay by doing water changes or by using approved chemicals.
Hardware/setup can be the same.