1. I always assumed this to mean to same as you say, i.e. a player like you or I can have multiple characters (as created in the login screen) in different factions. As for not being allowed in more than 2 system owning factions.... hmm I guess that's in place to minimise conflicts of interest between your multiple chars. It's probably one of the "lesser known" rules.
2. Dunno.
3. "Factions and faction members (just like all other players) are obliged to act in the way their reputation and status require" ... this could equally apply to the rep/status between players factions, as outlined by their posts in the status thread. Rather than the NPC factions represented by whatever ID they carry. So it may be ok.
