Here is the USB to Serial portion of Sparkfun's Stepoko board. Can anyone help me understand why the USB power is isolated from the +5V which is a separate onboard supply powered by an external supply? Nothing except the FT232 is powered by the USB. Hence would it be ok to just leave the F_SMALL fuse and D3 schottky diode unpopulated? Why do you explicitly need to isolate the two supplies?
If Vcc is higher than +5v + the forward drop of the diode the board will be powered from USB. If +5v is higher than Vcc - the forward drop of the diode then the board will be powered by the on-board supply. By removing the diode and fuse you remove the ability to power the board by the USB port.
You must isolate the two power sources because a USB device is not allowed to drive power onto the USB power lines. Only a host or hub is allowed to do that. The diode prevents the board power from going out through the USB port.