Sure, we could replace the core plugin of the server (TotalFreedomMod) with dozens of off-the-shelf solutions, but at the cost of what? That plugin has several components that off-the-shelf plugin could never possibly replace, including the magic of this server.
Multiverse doesn't add any functionality that lets you generate worlds; that is already built into Bukkit itself. All that plugin does is make the process of creating new worlds and navigating through them more user-accessible, and even then it simply cannot generate worlds like the Flatlands on its own because it doesn't know how to generate them like it.
You know how when someone gets smited, banned, or doomed, it shows a message that calls them a "naughty, naughty boy"? That's been in the TotalFreedomMod for literal decade, and has become part of the charm the server has. You would never be able to recreate it in an off-the-shelf plugin. Never.
The TotalFreedomMod gives admins some very important tools that have been specially-catered to this server, which have since become mission-critical for administrators because of their versatility. Plugins like EssentialsX would never be able to replace those tools because often times said tools are hardly useful for servers that aren't like ours (in other words, most servers). Replacing the TotalFreedomMod with EssentialsX would end up leaving admins without tools they frequently use on a daily basis, which is bad.
When people say we shouldn't use the TotalFreedomMod, they usually mean that they want a more stable core plugin catered to servers like ours that isn't buggy as hell and licensed under a prohibitive license. They don't mean that we should outright get rid of the core plugin that makes us unique in favor of generic solutions.
Object.