Got it now. I deserved the "presumably" and "Of course."

Thanks. It is the reverse of what I thought. With plexpass you can download the beta versions (at the moment .4.2865 rather than .3.2852), so the only difference between the two FreeNAS versions is that one points to the beta version and the other not. Eventually the stable one will update to those changes.
I had thought the plexpass version somehow had different features that were still in beta unrelated to the plex version you were on. It would have been clearer to me if this was described as "plexmediaserver-beta (requires plexpass)".
Partly because many threads like this talk about "upgrading to plexpass", when upgrading PMS to plexpass just requires a subscription, and changing to beta versions isn't really an upgrade.