I'm guessing the whole "sacred timeline" thing is artificial. They're forcibly trying to streamline the timeline(s) for some sort of cosmic convenience. It's how you end up with Red Skull being a stone guardian and, of course, an office full of copious copies of infinity stones. I'm guessing this is going to "end badly" and lead into the next Doctor Strange.
Another thought I have about this is that I think Loki in particular prob'ly bucks destiny a lot, and that there isn't just the "other one" running around. In fact, I'm also almost willing to wager this isn't the first Loki that Mobius has tried to or has succeeded in recruiting.