How is the boards list generated?
Arduino maintains the list and updates it every time a new core or tool or board definition is updated.
You can also add your own urls for additional (non-arduino) hardware in the Visual Micro "Configure Ide Locations" Window
At the moment, the IDE handles one URL only, and that's written into the code. This is a known limitation. However, if you know your way through the code, you can change that URL with another one.
Built-in cores cannot be deleted: they are part of the minimum setup provided by the IDE. However, if the built-in version is giving you troubles and a newer (or an older) one would solve your issue, you can upgrade (or even downgrade) a core, choosing one of the available versions
Arduino Hardware | Installation