Taking a look at the pcb layout, it seems as though disconnecting pins 4 and 20 from the +5V line would be close to impossible, at least for me. They are bottom copper directly under the FTDI chip, which is of course under the MCU on the other side. A physical intervention would require de-mounting the USB-serial chip and then re-flowing it and that's not something I'm about to try. Yes, Lefty, tying those traces to the USB power rather than the 5V post regulator would be less cumbersome than using a switch or jumper.
Time to figure out what it means to say that a host goes to USB standby, what the various power modes D0, D1 etc. mean, and whether the Windows API would give me a simple means to do it.
I guess the other thing I should do is to make up a USB cable with the 5V line opened so that I can measure current from an external 5V with the PC in various states: connected, standby, hybernate, un-plugged.