Earlier quoted context omitted.
The pop-ups and "social engineering" in question are things that any users in HN likely already accepted, which is to enable community plugins. These community plugins are the backbone of Obsidian and where a lot of the meat is behind its fame come from. There's no protections beyond that, community plugins can do whatever they want. Thankfully, the vast majority of them are open-source.
I'm gonna push back against the "backbone of Obsidian" part. I'll argue that vanilla Obsidian is plenty powerful enough. I know many people swore / swear by the datatables plugin, but now that Bases in core, you can get pretty far without it, no?
There's countless articles and videos about various community plugins and even curated selections of them depending on your use case for Obsidian.