The timeline is everything flowing. Every universe is simultaneously moving. The branches show that characters are behaving outside of their narrative. Being within that timeline just means that every Loki played their part. The Lokis that go against that are taken. It's not about appearance, it's the action.
Sylvie was born female. That is not where she went "wrong". She is playing with figures and mentions a win for a Valkyrie. I agree with the speculation that she is signaling the want to be a Valkyrie. it's still not confirmed tho. This is the action that warrant the TVA coming. Classic Loki said something similar. As soon as he attempted to leave and see Thor, the TVA stepped in. Kid Loki killed Thor.
Lokis are meant to do certain things whether alligator, black or female. Once they show they are willing to go against their narrative or "role", it's time for the TVA to step in. This was dictated by HWR. The role of a Loki was said to hurt others and make them greater in the end. Mobius explained this in episode 1.
I speculate that He Who Remains is trying for his base self to not notice the existence of a Multiverse. He explained that him and his other Variants came to know of the Multiverse at the same time (31st Century). That base form (MCU might go with "Nate Richards" as the name, idk) coming to that finding might be the key. In the comics, it was explained that certain moments in the past trickled down as part of how Nate got to the finding. Again, the MCU have no obligation to stick to this.
So, going outside of your narrative in any universe, might be part of how the Multiverse is detected by "Nate". Nate is driven by curiosity, as we see with HWR, he is enamored by Sylvie and Loki's interactions. So much that he allows for them to come because something about them gives him a leader of the TVA vibe. I think this can be a common "weakness" for Kang to be considered by the audience going forward. All Nate Richards can be curious to a fault. How do you write that without making Kang incompetent if he is to be the next Big Bad.
I'm honestly not buying it for now that he is the Big Bad, even tho he is clearly being positioned as such.
@Shiebs yes, there is 1 timeline. Meaning every Tony, Loki, etc have a role to play and stick to it within their respective universe. Appearance isn't a difference, but going against what your character is said to be, is a dramatic deviation for HWR. Once those differences/actions are detected, the branch is quickly pruned and the one triggering it is taken in. Not confirmed, but I believe the ones that can't be salvaged are pruned and those like Mobius are memory wiped for a TVA job.
I mean one Loki literally says he never met Thanos until that moment where he was supposed to die, shouldn’t he and his timeline have been erased if he never met Thanos, since that’s the way things were supposed to go?
Are you referring to Classic Loki or another 1? They don't all have to go through the same exact moments. Just have to play their part as chaotic and hurtful to others. Killing Thor as kids or trying to see him after exiling yourself are things that HWR looks at as a threat to the flow of things. I think the full picture of things come together once we meet Kang. His appearance will reveal what kept him at bay.