I might be mistunderstanding you but even if witches are the one who use some kind of magic that the creation of doppelgängers happen I doubt they have to be active "to create them" as once every few hundred years or so someone that is born in a direct lineage will be the doppelgänger, looking like the immortal they share the bloodline with.
As for doppelgängers in general it's true we only know of two bloodlines which we will probably find out about the other one is (let's say Silas's lover). Although it doesn't make much sense that he managed to make her immortal (for Tatia, Katherine and Elena to appear) too then she managed to flee as a human before Qetsiyah's wrath could get to her since she created the cure for Silas, she likely would know how to make too and would have forced fed it on the lover then killed her (but then her line would have perished because she lost her immortality). I think it's more to the story then Silas told us or that the legend said according to Shane. As it stands now Silas is only evil because he had to starve for 2000 years alone and he knows his lover died but I think his personality has always had this manipulative strike and I doubt (at least hope) Qetsiyah's only reason to wanting to destroy him was not simply out of jealousy.
Speaking of Stefan's soul, they never mentioned anything of that but I suppose the common rule in fiction (at least fantasy) that a living person is the container of a soul and when that splits open (at the moment of death) the soul is released so it's likely true what you say that when you die your soul or spirit moves on to a different plane. What's interesting in this though, it's more like a spirit than a soul because soul is usually the ethereal version of a creature's personality while a spirit is more fitting here considering Stefan is still Stefan and he acts as he did when he was human.
Or there are entirely different rules here. Now that Katherine took the cure maybe the magic essence in it did change her DNA that she's now basically a human but technically very old yet very young.
I definitely hope they clear up on the rules as it's interesting to understand the dynamics of how it all works and not just focus on characters and the story but also the lore and how everything is.