Me too!
This feels like throwing darts.
From the schematic:
It appears like that IO pin has a Pull-Down resistor hooked up to it. So setting it low should have no effect.
Sorry I know that it is covered earlier, but it is early in the morning, and I need a lot more 
to dig through thread, so will ask here.
How exactly are you building and uploading your sketch? Specifically what board type have you defined that is setup for the WIFI, but enables USB and uses the different bootloader?
If for example you are building as MINIMA, then everything we are mentioning about pin numbers and the like is totally bogus, as we are talking about a different pin table.
Instead of:
pinMode(40, OUTPUT);
digitalWrite(40, HIGH);
You might try:
R_IOPORT_PinCfg(NULL, BSP_IO_PORT_04_PIN_08, IOPORT_CFG_PORT_DIRECTION_OUTPUT);
R_IOPORT_PinWrite(NULL,BSP_IO_PORT_04_PIN_08, BSP_IO_LEVEL_HIGH);
Which unwinds the code for pinMode and digitalWrite to the specific port/pin and does not rely on the variant pin table.
@ptillisch - do you know if anyone has setup a proper variant for this?
Probably starting up as a copy of the WIFI, but then change the build options to remove the no USB define, plus the upload rules... Alternative might be an option under the WIFI to do this?