On Arlinn, her alternate artwork and the third story both indicate she still served the church, so either it truly was a bizarre slip up in the second story or the friend incident is congruent with her sparking (Innistrad werewolves go through a first hunt according to the planeswalker's guide, so realistically she can't first have exploded in the angel incident). I think these inconsistencies can be easily ironed out.
I think both the friend incident in the new story and the devil incident in the old story were written with the intention of showing her spark ignite. The thing is, her being pulled to another plane and away from the influence of Innistrad's moon is what helped her control her transformation, so the devil incident wouldn't make sense if the friend incident had actually happened before that. Besides, the author's reply sounds to me like she's acknowledging the probelm, or she wouldn't have praised the other person's "good eye". What's more, both events being "components of the same memory" would seem to imply that they are supposed to be one and the same event, or how else could they belong to "the same memory"? I bought new shoes today for instance, and I have
different memories of previous - but
different - instances when I also bought new shoes (once every few years or so). There is just nothing to indicate to me that this story was written to be compatible with the original one, and I honestly don't feel like making this harder for myself than the people who wrote and approved it made it for themselves.
On Tovolar, I was wondering about that as well, but on the mute thing they seem to be consistent since he barely speaks anyways, so it'd be easily to assume he's mute. His transformation is the issue, but I assume this is Emrakul's doing.
I don't think we can blame Emrakul because Tovolar clearly talks and transforms in those flashbacks that are set during Arlinn's youth, long before Emrakul was even freed from Zendikar.