It seems odd that they should place the action in Crestwood, which is one of the places that we specifically have to go to as part of the main plot, when they could have set in it any other village in Ferelden where the Inquisition hadn't reached or had only done so via their agents, rather than the Inquisitor themselves. There are plenty of Inquisition agents that they could use in addition to Harding and Charter does seem a likely candidate since she does end up running Caer Bronach, but the fact that Leliana appears on one of the comic book covers would suggest it is likely to be her.
I think it was strongly hinted that Samson was eventually going to be killed by the red lyrium, particularly with his master gone who had the knowledge of how to control it and his tranquil friend who had been responsible for the upkeep of his armour. So even if you did Cullen's personal quest and were able to capture Samson, whatever you decide to do with him, his fate is ultimately sealed.
Whilst we take one path or the other, I think the canon story is likely to be that those who died on one path, also died on the other, we just don't see it.
World of Thedas 2 states that both Alexius and Felix died in the south, when if you take the mage path, Felix can return to Tevinter to address the Magisterium before dying and Alexius can be made an agent of the Inquisition, although I suppose he could simply give up on life at some point after Felix's death. In fact on the Templar path we only assume they are dead, since Dorian states there is no sign of them and it is as though they had never existed, so you could assume that Alexius had tried to pull the same trick with the amulet against, say Calpurnia, and ended up sending himself and Felix into the ether. Anyway it would seem the main point is that whichever path you took, by the end of the game they are both dead, regardless of the means.
Calpurnia is more interesting since you never see her dead. On the mage path her fate is very vague. On the Templar path you either let her depart or she fights you and jumps off a cliff, but you never see her hit the bottom. World of Thedas 2 is also sufficiently vague about her end to make me hopeful that they could bring her back. Now if Marius is floating about in southern Thedas and still has feelings for her, then they could use him to explain her survival into the future. If you let her depart she intended confronting Corypheus about his deception, which she could still have done if she jumped off the cliff or you never even met her, so the two Mage Killer heroes stepping in to save her from his wrath might not be beyond the realms of possibility.