Proton rolled out the beta version of Key Transparency on their own private blockchain, meaning it's not run by a decentralized series of validators, as with Bitcoin or Ethereum. Yen said Proton might move the feature to a public blockchain after the current version serves as a proof of concept.
Because the Proton blockchain is currently private, the keys they are currently adding could easily be affected by a man in the middle attack.
No. That's not how that works. Just because a blockchain is "private" doesn't make it suddenly changeable, and it doesn't mean there's a unsafely small number of nodes. People commonly get invited to participate in beta testing; that's kind of how software development works.
And there would be no way to invalidate those keys for any of the affected users, ...
Remember when I said:
As long as there is an appropriate method for adding a legitimate entry to the chain, incorrectly entered data can be handled by appending corrected data on to the chain, and marking the error as such.