Well sir, to be fair, PHP is PHP. The question is whether or not PHP is supported on a given operating system. And I believe it is, for FreeBSD.
As for the security question about out-of-date plugins---typically speaking you should not be opening up your owncloud to the WAN without a VPN in any case, so that in principle, the security question ought to be moot. I myself generally concur that the burden of expecting the FreeNAS guys, or guys once-removed from the ixSystems guys, to maintain up-to-date plugins is a lot to ask. The plugins are a convenience. Any convenience has a price, especially conveniences that cost you nothing, and even more especially conveniences intended to bridge a gap between functionality and understanding. In this case, the price is not being as up-to-date as one might be with the underlying package.
This is why a lot of us don't actually use the plugins---rather, we make our own jails, install our own software from ports or packages, which means you're as up-to-date as anyone can be in FreeBSD, and thus, we have whatever the latest stuff is on the FreeBSD platform.
I have, for example, never used a "plugin".
But I do want to return to this important point: security updates to OwnCloud should be largely moot. Either, you're being security conscious, and can only access the OwnCloud from the LAN or a VPN, (which makes security updates mostly moot, unless you don't trust people on your own internal network, in which case you have bigger fish to fry), or you're not being security conscious by opening your OwnCloud to the WAN, in which case having the most up-to-date security patches is probably the least of your worries.
Bottom Line: Vigorously up-to-date Plugins are almost certainly not going to be happening. The solution is to maintain your own software in jails, if such things are important to you.