When linking more than 2 channels together message appears on all of them about cross-server-bot HOT 2 CLOSED

If I'm understanding correctly..
Each guild is supposed to have 1 linked channel, and that you can cross-server between multiple guilds instead of multiple channels inside each guild. So therefore looks intentional.
What it's doing is going through the guilds object in the config and sending it to every one of them which isn't the origin channel. What you've done is add a server on that same guild, meaning a webhook will also be sent there.

from cross-server-bot.

Yes indeed. You can't have multiple network on the same instance as of now.
As noted in #5, this is the current intentional behavior.
However this will most likely be added in the future.

Right now the only way you have to do that is to host several instance of this bot. You can even do it on the same token if you don't want to create another bot application.

from cross-server-bot.