They're saying that technically accurate or not, the article is misleading and doesn't give context. In particular, this supposed threat is almost impossible to exploit in practice, as it requires the attacker:
1. Knows exactly when you're going to swap a SIM card over or otherwise change phones
2. Also knows you simultaneously have a bunch of messages waiting to be sent, that the attacker actually cares about.
3. Also knows that you have gone into settings, and unchecked a setting that would normally be checked that warns you if a change in encryption keys has occurred
4. Has access to all the infrastructure in the middle.
That's a tall order. It'd be easier to just steal your phone, or hit you on the head with a blunt instrument XKCD style until you talk.
The letter also points out that the article discourages people from using a popular messaging platform over this issue whose security is generally first rate, encouraging them to seek alternatives that either may be insecure, or may be taken as a sign of guilt (eg Signal), making it easier to pinpoint dissidents with something to hide.
So, yeah, the article may be technically correct, the best kind of correct, but if it leaves people with a false impression, then it's probably right to withdraw it.