If you disassemble it then you have to mask off the threads on the shank and inside the action as the buildup of paint (which is all Duracoat and Cerakote is) is enough that it will create a problem. That combined with the need to touch-up the work after re-assembly makes it a no-brainer to just coat it as an assembled barreled action. Quality and durability of the finish won't make a difference either way.

Now, if you want to tear it down for the prep work, that's another story as the prep works is where it's at when it comes to getting a quality finish. Just reassemble before coating.