Indeed, you are correct:
By default, this value is false. If this is set to true, then MCEBuddy will ignore the Copy Protection flag on the recording if it encounters it during conversion. It will only record an error in the conversion log and continue the conversion. If the recording is really copy protected then the final video will be look garbled. This flag can help because sometimes videos are incorrectly flagged by recording software/tuners. When this is set to false, if MCEBuddy encounters an Copy Protection flag it will stop the conversion after logging an error.
I've never had it checked because ALL my recorded material arrives via antenna - in a realm where the broadcasters want me to see, record, use whatever they broadcast in whatever manner I choose.
So I guess, in the end, Plex-DVR can only be used with a reasonable success rate by employing an antenna where most, if not all, of your material will arrive without restrictions baked into the cake. It's not surprising then that the documentation available on Plex-DVR is vague, but to your credit you are recommending wildly overpriced antennae that are little more than a 150 dollar coat hanger.
In reality those living in an urban area would do well with this 'Mohu' ($150.00) - or with a well tuned coat hanger ($0.14), but there will be no 'Premium' cable channels arriving over the airwaves. That will require a wire and what is sure to be a fair amount of disappointment from Plex-DVR.
And to be fair - this isn't Plex's fault. They're just playing the hand with the cards they're dealt. I'm sure Plex-DVR from antennae is going to be very nice if what you want comes from NBC, CBS, ABC, PBS or other OTA Broadcasters. There's plenty of stuff to receive freely in eyeball blistering High Definition the likes of which you will NEVER see via cable.... albeit not what many are expecting.
Those in Urban areas, or more remote locations within the United States (maybe Canada) can visit: http://www.tvfool.com/ , plug in their address and see what's available and extrapolate a game plan (antennae shop) to find out what would be necessary to receive these digital broadcasts so they can enjoy Plex-DVR to it's fullest.