Perhaps the TVA is a cover-up? If Kang really is abducting so-called Variants to make TVA members, then to what end? Sure, he wants to control & optimize the timeline for his conquest, but we've seen that the TVA members are individuals, capable of independent thought, even when their minds haven't gotten magically muddled; Mobius was convinced to betray with only things already in the TVA & words.
If you want an army, free-willed individuals like that aren't going to be optimal soldiers, especially if your cause is something "evil" that they may disagree with.
But if you want to control a timeline, let alone multiple timelines, if you're openly evil, even with subterfuge, you're bound to get individuals, not just traitors among your ranks, but from the timelines you oppress, coming to oppose you.
Ergo, the TVA wouldn't serve if they thought/knew they were working for an evil cause, & even if they did, the timelines you send them after to would eventually start causing problems for you; Even with anti-magic, "sufficiently advanced technology is indistinguishable from magic", they say, after all.
Hence, the TVA has to be a cover-up. Make those who are problematic for your "Sacred Timeline" into the TVA members, who believe they were created by it, & aren't very important.
But the actual threats? The Nexus Events?
Tell the TVA to bring them here, & "prune" them; It's true that, when they use a timeline pruning/resetting device, it seems to erase/reset things....
But perhaps it is different for people than things, or different inside the TVA than out of it, or different before the timekeepers?
Either way, the purpose seems clear: When you find a serious threat you want to recruit for your ACTUAL evil army, hidden even from your already secret organization, what better way to conceal their recruitment than to erase them?
Maybe in certain circumstances, the "pruned" are actually teleported, to be brainwashed? & from there, they are to become Kang's TRUE evil army.
....Or something.
Of course, there's other possible explanations. Maybe the people we see in the post-credits scene are other Variants on the run, rebelling against The Timekeepers. Maybe they found a way to mimic the technology? Intercept the signal & teleport someone out of their would be erasure-by-pruning? Or a way to fake it appearing to happen?
Or perhaps, probably most implausibly, the system is flawed, & Loki was only killed physically, & his soul was able to be relocated, perhaps into a body? Admittedly, this is far-fetched, & is mostly a half-baked inferrence on my part, based on the dialogue "Is this Hell? Am I dead?" "Not yet. But you will be, unless you come with us."
I will admit, it takes a few leaps in logic to come up with & perhaps even believe this speculation of mine, so I'm very much open to other people's opinions on when we saw Loki get "pruned", seemingly being erased, yet then awaking somewhere else, apparently alive, & seemingly in danger, surrounded by oddly familiar faces who say he should go with them for his safety.
