This assumes total control of all commands that are attempted, even ones that are not registered through it.

Sorry yeah that first one isn't all that clear...

The discord side of things seems to assume total control of all receiving of messages, I have a secondary discord bot using the same bot token and with this one running that one no longer reacts to commands I have programmed into it.

This is specifically the discord part of it, not the minecraft side of things.

Could you clarify what you mean by this?