SOLVED - The categories/channels were set to private which is why they couldn't be changed even with the correct permissions. My solution was to tell the user which ones and to add the role with the permissions manually. I added a message that said they can just give the bot administrator permissions and it will do it for them. Hopefully, this helps anyone who runs into this in the future.

I'm trying to change the permissions of multiple categories and channels using the following code:

role = get(guild.roles, name="Fun")
for channel in guild.channels:
    overwrites = channel.overwrites_for(role)
    overwrites.view_channel = False
    await channel.set_permissions(role, overwrite=overwrites)

I get the following error:

await channel.set_permissions(role, overwrite=overwrites)
discord.errors.Forbidden: 403 Forbidden (error code: 50013): Missing Permissions

It will work if I give the bot the administrator permission. However, it won't work if I give the bot every single other permission, the bot is at the top of the roles, and it has every category permission. What am I missing? I'm using Novus (fork of discord.py so it's pretty much the same thing).

Edit: I've asked people in the discord.py, Novus, and discord developers discord servers and they can't help me either. With the exception of the discord developers server they just didn't answer my question.

Edit 2: I was able to get it working when I manually added the bot's role to the category and enabled view_channel. This won't work, however, because that means the server owner has to manually do this for every category and channel which is really inconvenient.