Question
- Can Rpi interface with MicroBit over GPIO? 
- Can Rpi interface with MicroBit over Serial? 
Short Answer
Yes, no problem at all.  I would suggest to start with UART serial,
  using Rpi python on one side, and MicroBit MicroPython on the other
  side.
Long Answer 
Brainstorming comments
- I played with MicroBit a couple of years ago, mainly using microPython.  My MicroBit knowledge is a bit out of date.  I need to
  google and do some tests to catch up. 
- Using Rpi and MicroBit GPIO to communication is possible, but only for very basic communication and control, say this side reading button
  presses at the other side, or another side blinking LED at this side. 
  For more complicated things, it is easier to us UART serial, because
  the handshaking, message sending and receiving protocols are standardized. 
- Though both MicroBit and Rpi have I2C and SPI. but usually both behave as masters.  It might be hard to make changes to let two masters to talk
  together. 
- For easy troubleshooting, it a good idea to do 3 steps:  
     (a) Make sure Rpi UART/serial software/hardware setup/initiation is OK 
         by checking python serial loopback. 
     (b) Make sure MicroBit also OK by microPython serial loopback.
     (c) Make sure WinPC RealTerm 9,600 8N1 can talk to Rpi.
     (d) Make sure RealTerm 9,600 8N1 can talk to MicroBit.
     (e) Now the time has come to let Rpi and MicroBit to talk to each other.
- So far I have not read any good tutorials on Rpi talking to MicroBit, but Rpi to Arudino are plenty.  You can easily google, or read the
  posts in the references below.
References
BBC micro:bit MicroPython Docs » Microbit Module » UART 
UART on Micro:Bit - MicroPython Forum
Rpi Talks to Arduino Over UART Serial - Rpi StackExchange
Appendices
Appendix A - MicroBit PinOut
