Niche communities are easier for a small handful of volunteers or employees to moderate. There's simply less shit to clean up. Compare that to Facebook, Google, etc; all of whom have to hire armies of moderators who will burn out in a span of months. The attrition rate is very high, and there's just too many moderators to have consistent platform policy enforcement.
Furthermore, if someone is just there to be toxic, you have an easy justification to shut them down: "I'm sorry, but this is an underwater basketweaving Discord, please stop spamming #offtopic with why you think we should call in the National Guard to fight the war on Christmas." Many small communities have very strict regulation of political speech purely because it causes most of their problems.
Alt-tech is trying to collect all of the toxic bullshit in one place, so obviously they're going to be way more toxic despite their small size. It's also possible for niche communities to have their own toxicity problems, too. It's more that large communities are just inherently more difficult to govern.