It would seem to me that a whole bunch of things are thrown in together here.
Suppose I can drop my two cents of experience as a faction lead for a quite some time around. Granted my case might be more of an exception than the rest considering the type of faction and historical reasons. The only faction right I think of ever using was fourth one in the current list, basically moderation of in-game events to ensure trolls wouldn't crash it, but that's about it really.
As I'm trying to remember I think one of the reasons ppl actively wanted their factions to become official was to have a guard system and kinda set their little paradise there. Granted it did result in some seriously botched stuff that is still giving plenty headache to fix it, but you know, there was a certain sense to that, in a way it was a showcase and factions sure loved that kind of involvement, even though those were typically dead end systems, so function-wise those were superficial things. That makes me thinking now... If there was more advanced POB system with branching types and such, like say you could upgrade into a mining type POB, or a research type POB, or a military POB, and so on, each with own type of benefits, then I'd say suppose it might have brought that sense of, you know, tangible accomplishment and visible thing around, a continued presence of sorts. But then there are people who keep telling POBs should be removed as a whole. Me, I don't even have any stakes in either way, can't build POBs as nomnom anyway. :-)
As for the rift, I think it's already visible just by looking at the "player faction"-specific IDs. As I remember at first back in old days those were scooped up, leaving only a very few mostly due to technical constraints and not for reasons of separation between a player faction and their indies. But what you see more around now are more examples of separation away from generics. After several notable examples in the past when officials got wrist-slapped when they tried to make gradual change say in diplomacy with another faction, but indies would simply ignore that process, not necessarily out of ill intent but simply because they were unaware. However the problem began when say they were made aware of the process in diplomatic shift some would just ignore that on purpose. As expected that can quickly spiral out of control. And as a faction there really ain't much you could do about that. But if you try you'd likely get slapped by admins as it were before. So I don't know, to me personally, unless there is a technical necessity to separate between indies and faction, there shouldn't really be this growing apart process going on now. Keep in mind, in this case I'm more of an observer really, having talking to other faction leads, hearing them out, what problems and difficulties they are facing, talking to indies who have their own frustrations, desires and such. But given that nomnom stuff in that regard is completely different I think other experienced leads may provide better insight into the subject of why there is a growing number of faction-specific IDs.