As far as I am aware, the only way to connect between Scratch 3 and the BBC Microbit is to use the TSR program ScratchLink.exe which provides the interface between Scratch 3 and the Bluetooth Low Energy stack together with special firmware loaded onto the Microbit to implement the Microbit end of the BLE and ScratchLink protocol. This is what is used when you load the BBC Microbit extension to Scratch 3. it offers the 'When button pressed' (A, B, Any), 'When moved', 'When tilted', and 'When pin x connected' events plus the ability to send 5 x 5 matrix to the Microbit LEDS, and display scrolling messages on the Microbit LEDs. Essentially allowing basic support for using the Microbit as a peripheral to Scratch 3.
However, this is currently only available for a Windows PC and as yet not for the Raspberry Pi. It takes significant understanding of the BLE stack on the Scratch host system to implement it so I would suspect that it would require significant input from RPF to create a Pi variant of it. Furthermore, I have as yet not managed to locate the specification for the ScratchLink protocol.
I have already asked the question as to when it would be available for the Raspberry Pi in an earlier post and was told to ask MIT.