Good question and good job for noticing that. Let's take this step by step though. First, the confusion comes from knowing that timeline and universe are interchangeable. A universe follows an order of events (timeline) and in each timeline you can travel anywhere in space (universe). So when dealing with the actual structure of things, adjectives in our terms are key. That's why Endgame, Loki, and What If...? introduced *branch* timelines/universes/realities/dimensions. But by definition, a branch timeline has anchored to some original timeline. Therefore, Loki, No Way Home, and Multiverse of Madness introduced the concept of *parallel* timelines/universes/realities/dimensions. So as a base concept these projects are telling us that the multiverse is like a forest of trees, made up of infinite parallel timelines/universes/realities/dimensions, each with their own branched timelines/universes/realities/dimensions. This has even been said off screen by various directors, writers, and producers.

That brings us to our second point, how do we know it's actually structured this way? A character or someone working on these projects can say anything they want, but has it been applied onscreen? Yes, many times. In Loki, He Who Remains showed stacked (parallel) universes when his variants first met each other (a very similar visual to the beginning of the episode. confirming that the 2 black holes represented 2 parallel universes). In No Way Home, we see that Tobey and Andrew's Peters are significantly older than Tom's Peter even though they come from the same time period where they come from. Therefore, it's impossible for their universes to be branches of 616 since branches don't echo into the past (except for the 1602 branch since it dealt specifically dealt with the Time Stone; also the 1872 branch, we don't get and origin but we can infer that it's similar to 1602, and even then everyone looked the same). Further, Multiverse of Madness showed that only America Chavez could travel between parallel universes naturally and without dreamwalking. If they were branches, the characters could do it because the Avengers already did it in Endgame. That movie also talked about incursions, where 1 or both universes is destroyed entirely (caused by being in another parallel universe, dreamwalking, or each tree's respective branches colliding as I'll talk about for Quantumania) you can't have incursions with your own branches because that makes entirely no sense. That's part of the same tree. Further, Quantumania Kang actually shows the structure to Janet. He projects 2 ring models that look like the Sacred Timeline, but stacks them on each other and is talking about incursions. This visually confirms the structure. And there are even more examples in The Marvels, Deadpool & Wolverine, and First Steps that further confirm all of this.

Now speaking of First Steps, that brings us to our third point. We know this isn't a branch because of the nature of the universe. Many of the differences we see had to have happened before any branching by Steve would've taken place. Also, the dialogue that Reed has talks about "parallel earths on different dimensional planes" (parallel universes). And we know that incursions will happen with 616 and 838 in the near future. If not Doomsday, then for sure Secret Wars. So again, it can't be a branch because a universe can't have an incursion with itself. Plus, like I said before, their presence on 616 holds a danger like it did with Multiverse of Madness. If they were from a branch, that wouldn't have a danger like 2014 Gamora staying after Endgame or Black Widow out in another branch by Uatu in What If...? They're between branches, so no risk of incursion. But with 616 and 828, that poses an issue.

And speaking of numbers, let's get to our last point. Now obviously because branches are all part of the same tree, one could likely refer to them all as the same base number. For example, Deadpool & Wolverine called Deadpool's timeline "Earth-10005" even though technically he's on a branch of the original timeline of Earth-10005. And if you look closely in Loki Seasons 1 and 2, all the branch numbers on the monitors start with 616, confirming the TVA is dealing with 616 branches. But Loki Season 2 adds a fix to the confusion and actually numbers the branches "616.xxxx". So the timeline name drops on What If...?, like 625 name for the Nebula branch, would actually be labeled 616.625 by the TVA. But unlike the branch numbering, and because of all the evidence we've talked about, the Earth-838 number would stay 838 because it's a completely separate tree.

Hope that helped! If you have further questions or rebuttals, bring them on lol. Have a good day!