I see what you mean, but look at it this way as well. Someone in the official faction doesn't carry the tag AND doesn't have the official ID. Not only is it not counting towards your faction activity, but it also allows for you to do actions that would allow your official faction to get away with it. What is stopping your entire faction then running tagless AND ID-less from doing something unlawful, or doing something that normally you couldn't do on your official faction ID/group. For instance, let's say a Junker is smuggling Cardi. He gets stopped by police, and yadda yadda yadda RP's. He's hiding he's in the <INSERT JUNKER OFFICIAL FACTION HERE) but not flying the tag or ID, thus the actions are pinned on him. Now, say then the entire faction has a regular Junker ID and no tag, but they are still in that faction. No one knows such then, and the group can get away with anything because inRP no one can prove they're all the same group. Say also the Junker official faction made enemies with a specific group. A bounty is placed on them. But, they don't fly with the Official ID and don't fly with a tag. That bounty then can't be claimed, and they are getting away from any repercussions for their actions.
Same can be said on the other side too. They made alliances, and that tag is allowed to dock on a base. Or they've made a deal with another group that normally hates Junkers, but they're lenient with this group. If they don't have the ID or tag, how will they know? These are just examples off the top of my head, but you see the point i'm trying to make. It allows for more, I wouldn't say abuse, but more ability to get away with actions without the repercussions or benefits.
While many yes are copies of the NPC ID, they were made to signify you're in an official faction, and say your faction becomes rep-hacked (Good or bad), the rephack is based on the ID, not the tag. So if said Junker group pisses off say Corsairs, and the Corsairs put in a request for rephack change, it only applies to the Official faction ID, but if you're running the NPC ID, you're circumventing the rep-hack.
That make sense? I get what you guys are saying, but being able to fly either ID opens up the possibility for abuse/circumventing the results of RP/actions your faction makes, whether by your choice or someone elses.