I have a custom installation profile and my default theme does not have a 'help' region. System module defines a block 'System help' which tries to automatically assign itself during the installation into the 'help' region.
But since my theme has no such region I'll get the 'The block System help was assigned to the invalid region help and has been disabled.' message.
In the system_block_info there is a comment '// Auto-enable in 'help' region by default, if the theme defines one.'. The last part is basically ignored.
So I think the failed attempt should not trigger the status message or it should check if the theme really defines the 'help' region like it says in the comment and only attach itself into it when it is really defined.