X and US law both have rules against incitement of imminent violence. It's one of the only exceptions to the First Amendment. X extends that to making violent threats in general. Those accounts were doing the latter and sometimes the former.

The @vps_reports account named in the first tweet in your story is a good example. The Intercept claims they were suspended for engaging in "journalism", "organizing" and "documenting extremism". X claims they were suspended for making violent threats.

If we follow links a bit further we see what sort of tweets @vps_reports was making:

https://twitter.com/stillgray/status/1596074770193604609/pho...

> "One last thing. ChayaRaichik10 should live in fear for the rest of her days. It's only fair. Put the PHOBIA in her transphobia."

(there are several more examples like that)

It's not surprising that such people would fall afoul of an anti-threat rule if enforced fairly. Pre-Musk, people like that could make violent threats on Twitter, or even coordinate mob violence there, as long as they were threatening right wing people. Musk fixed that. The Intercept is being dishonest.