The story explicitly tells us, several times, that the entire branched reality is sent to the void.
Then there was this entire exchange
The show only depicts certain items showing up in the void, because from a practical standpoint, how do you an entire universe full of matter arriving on a singular landmass? As a point of reference, It's much easier to show a few remaining scraps rather than Alioth's entire meal.
As far as it appearing that reset charges only prune the local area- think about perspective. If an entire planet is being moved to the void, along with the universe it exists in, how would that look to a camera placed on the planet? It would percieve no change at all- just like we don't percieve our solar system moving around a black hole. My guess is that the items we see getting "reset" are actually the items the TVA keeps while the rest of the reality is sent to the void. It would explain Renslayers collection of items, including the pen from her own pruning.
the concept of removing a few items, a single person and restoring the timeline to its intended path, variant and all, was propaganda that turned out to be a lie.
I do agree that there's dialogue in the story that says they destroy entire realities, or universes, but I just think they mean they prevent those realities from ever existing, not that they send it to the Void or destroy it.
Take in mind they erase those realities that are created
after a Nexus event though. Supposedly, they didn't delete the original universe where Sylvie was born, just the universe that was created after her Nexus event (which still remains a mystery, but apparently has to do with her toys). We see this in The Void.
What I wanted to communicate with my original response, was that the show, for storytelling, visual, and maybe even budgetary reasons (although I don't think it's so much a question of budget) shows us the TVA only deleting certain items, some as big as Pyramids or spaceships, from the Sacred Timeline. The Sacred Timeline, by the way, might have or might have not been be actually just several very similar timelines woven into a rope, that are compatible with He Who Remains' goal of avoiding more variants of Kang.
Eliminating Sylvie and her toys avoided the creation of another timeline, but that doesn't mean that they pruned the entire timeline that existed before her Nexus event where Sylvie exists.
In the end, like someone else said here, time travelling stories are difficult to really get right down to the last little detail. The true nature of time is difficult for us to comprehend, much less in a story made for a tv show that wants to attract a wide audience. We have to watch these shows knowing there are limits to just how precise they can be about the rules they set up. Just like in any other sci-fi show.
I think overall, Loki has been able to make coherent rules to the multiverse and how the TVA operates.