According to the official info, Dran seals the Fangire souls and uses them to sustain the Arms Monsters; of course, this hits Fridge Logic when Emperor Form starts destroying Fangire outright - what about Jiro and the others?
They go out and kill people, I...guess...
But they are confined to Doran... I... think... The writers weren't thinking straight, were they?
They can't be, Jiro leaves Doran several times across the 2008 timeline. Not for very long and usually only to take someone else to Doran or to give Wataru some important bit of knowledge he needs but he still leaves.
It's possible he destroys weaker Fangire offscreen for that. Wataru's not stupid.
A lot of times, the "manual" is not written by the show's writers or consulted by them, at least in American works. If it's no different for Japan, it could be that this just isn't at all canon. After all, how often is the Fangire soul thing actually mentioned in series? At some point they stop Engaging Chevrons by showing the eating of it, but there's no discussion of "this form shatters 'em but leaves the soul, that form destroys both" or "this is the Arms Monster meal ticket" in show - ever. In other words, it's all Word of Dante and not Word of God.