Yes. The actions of the sub's moderation team are distinct from the actions of Reddit admins. AutoMod is run by moderators. And specifically that subreddit hates the admins.

I mentioned this elsewhere - but Reddit has shown they are willing to ban places for the smallest perceived slight. That subreddit is used to coordinate the protests (alongside a private Discord for mods).

My guess is that AutoMod is aggressive on that subreddit because the admins are going to be looking for an excuse to ban it and the mods don't want to give them one. So by setting an aggressive AutoMod, the mods can keep the community focused on its purpose - moderator coordination - and avoid the potential of a false ban for so-called "harassment".