Yeah the problem here is that those cats don't have a shit to do with canon, while Magus living or dieing does. If that's the case, they should have made an option at the start of CC: "Did you kill Magus in CT or not?" If the player answers yes, Lucca will say they killed off Kid's dear sweet brother at North Cape cause he was such an ass, and Guile would never be in the game in the first place.
You're not getting it. I know it's non canon, but
CANON IS NOT IMPORTANT HERE.
It's how the game threats what happens in endings according to what you did in game.
- Magus being dead or alive (making Frog become human)
- The Epoch being destroyed or not
- Lara being able to walk or not
- The number of cats, etc
If shit that doesn't have to do with canon gets enough attention to be consistent from in-game to end-game content, big shit like Magus being alive or not should get MORE attention.
If Magus from your party dies, no matter what is canon and what not, if the Magus from the new ending was him, he wouldn't appear because he was already dead. Due to the way that CT manages its consistencies of events, EVEN NON CANON ONES, the Magus from the Time's Eclipse can't be the same one from your party.
So he's not the Magus from your party, he's either the Janus we saw in CT as I stated, or an alternate dimension Magus.
And speaking of canon, we're still not sure if the new ending is counting towards canon or not. I'll go with FaustWolf and say no for many reasons.