Hello, The Tone Board’s schematic shows the switch logic concerning power input and source switch. See pages 3, 5, and 6.
These will need to be considered. I personally would not cut off the pins, at least for testing. For testing, you can use the schematic(GPIO section) to jumper GPIO connections to/from the VIM3L and TB. Not all GPIO pins are used, so you won’t need 40 jumpers. 
Much has been discussed on external powering of the TB, seems they had a slightly different goal, but may be helpful to read through it.