So Iga's timeline stands regardless then eh.
Not so fast. There is still evidence for Shaft not having been killed in Rondo. That being Death and not Shaft is actually one of TWO points I made. And I actually covered the second point (check the edit on my previous comment) which got me quite confused.
You mention this "IGA timeline". Is this the timeline you mean?
http://www.vgmuseum.com/mrp/cv-por/packaging/timeline-side2.jpgBecause, if it is, it is not correct in some regards, and is not the most recent. By the time IGA released Potrait, it was already known (and even mentioned by the man himself) that Circle and CV64 were not canon. And this is not the only info wrong in this timeline. I don't think this timeline was issued with IGA's final revision/approval of it - this could be the job of the localization team alone, and we know what happens when they get their grubby hands on these timelines.
Now, I'm not saying the ENTIRE timeline is worthless due to this specific bit of info. Much on the contrary, I think there certainly are very interesting bits of information there that do correspond with what we know of the franchise (even some of the most obscure bits of info such as the existence of a sixth Dracula Remain in Simon's Quest). What I'm saying is that it certainly looks a bit sketchy considering the presence of non-canon info and incorrect minor info in there, and that there is a more recent timeline.
In this most recent timeline (2007), it says that "Shaft had NOT perished" on the entry for SotN. Sure, by "not perishing" they could mean in a more general sense (he was killed, but not defeated), but there is no mention of Shaft "being a spirit" or "returning as a spirit" or any mention of his orbs, and it's weird to say he "hasn't perished" when he looks quite perished there on the floor after taking a beating from Richter - meaning that, perhaps, indeed he hasn't been killed:
http://www.konami.jp/gs/game/dracula/product/data.html