I think the only concern is that PBI and ports don't intregrate.
For example if you install Firefox 1.5.x from a PBI the FreeBSD system won't act as if one installed www/firefox and it's dep's. The good part is the PBI keeps all of it's dep's in it so changes to PC-BSD and the software enviroment via ports/pkg generally won't interfer with it. Like breaking it when toying with GTK+ ports ;-)
Beta versions can't be (offically) upgraded to the release version.
I also think that PC-BSD enables a SSH server, CUPS printing system and Samba Client by default.