Sub-theme adding prefix to all block machine names
You can't. 

This behavior is core functionality from the Block module that's enforcing its data model. Each time you place a block, you're creating a unique Block entity that has a theme property tied to it. Thus, the mainnavigation block entity can't simultaneously be used on the default theme as well as theme3. 

This is why Drupal defaults to generating ${theme_machine_name}_${block_machine_name} so the user doesn't have to think about it.