I have a multisite network and installed Automessage on one of the subsites. I enabled it for that site only and created a user message. When new users are created on the main site they receive the message even though Automessage is only enabled for one of the subsites.
If Automessage is enabled for a single site, it should only send messages to users who join that site, or at least there should be an option to choose this. I assume this is a bug.