Both of them are interesting reads. I find a natural cause now more plausible after reading them.
Yet, of course nobody knows and we might not for a long time (or never).
Pekar et al. do some complicated phylogenetic modeling that purports to show the MRCA in humans is too recent for a single introduction. That result is unintuitive, and I believe their model is highly suspect, per my comments and links at
https://news.ycombinator.com/item?id=32740568
I agree that "of course nobody knows", and so do Ebright and Chan; they are careful to assert only that further investigation is required, if necessary by subpoena (e.g. for any sequencing data potentially containing early genomes of SARS-CoV-2, whether as the deliberate target or from contamination like those Antarctic soil samples).
The author of the thread that you're praising does not though; she considers the question closed, and has viciously attacked those calling for such investigation, including Chan, whom she called "an intellectually dishonest, manipulative conspiracist". (Ebright gets rather unpleasant himself, so perhaps one could excuse her behavior to him as tit for tat; but Chan does not.) I find both those attacks and the overselling of Pekar's result to be deeply unfortunate. Don't you?
Have you looked at Pekar's full model, as set out mostly in the supplementary materials? This isn't any standard molecular clock approach. It's a byzantine stack of plausible but somewhat arbitrary assumptions, ending in a simulated phylogenetic tree. The shape of that tree with one introduction doesn't match the shape of the actual tree constructed from the earliest real samples in Wuhan, so Pekar concludes there were two introductions. But I'm not aware that such an approach has ever made a successful prediction, and there's no circumstance in any field where I can imagine trusting a model of such complexity without validation. Their sensitivity analysis is meaningless, varying some irrelevant parameters but keeping what seems intuitively like the main determinant of that shape (the connectivity of their contact network) fixed.
You are correct that Alina Chan's thread doesn't address that aspect of Pekar's argument. Others have though, per the Twitter threads I linked. What do you think?