they just copied IRC without understanding why it was that way

I believe it was clearly inspired fully by Slack, rather than IRC. I don't think there was anything they copied from IRC specifically, and nobody in their target audience (gamers) was using IRC at the time discord blew up, so I don't think that was their intention

But I agree it is a silly use of the word "server" to refer to groups of channels. Internally Discord actually calls them guilds. Server might also be gaming lingo they were targeting (so people would think of joining a Discord server as akin to joining e.g. a Minecraft server)

I actually like the top-level server structure. A community has user roles which control access to certain channels, the permissions can be either channel-specific or server-wide, and the roles are hierarchal with permission overrides specific to users. It makes it possible to have public chats with tens of thousands of users not be overcrowded, and have content organized into different spaces (memes, media, help/support, general, etc.) which just couldn't be done on Skype, which was all people in this demographic were using at the time. And the idea of hierarchal management of permissions and roles allowed moderation of large communities, so everybody moved due to convenience.