Here is what I did and the results that I get:
(1) I have a G80TH with COM1 Tx/Rx pins connected to a GHI USB-Serial Gadgeteer module. That is connected to my computer’s USB port with a mini USB cable.
(2) This shows up as a COM port on my computer. 
(3) I also have a micro USB cable connected to the USB client interface of the G80TH for deployment/debugging over USB. The G80 shows up in Device Manager. 
(4) Using the USB interface, and can deploy and run my application just fine. 
(5) I connected the MODE pin (PE15 on the G80TH) to ground, and reset the G80. Device Manager refreshes and the G80 is not longer shown as a USB device. 
(6) I open FEZ Config or MF Deploy. In FEZ Config I select the COM port in the dropdown and hit Advanced > Connect (or F5). It says:
Connecting to COM5
Failure - Device is not connected or not responding. No response from device. 
If I use MFDeploy, I select the COM port and go to Target > Connect (or press F5). It says:
Connecting to COM5…Connected
But when I press Ping, I get:
Pinging… NoConnection 
(7) Resetting the G80 while supposedly connected via MFDeploy also does not show any of the output from the G80. 
(8) Deploying doesn’t work either. 
(9) If I close FEZ Config / MFDeploy and connect to the serial port at 115200 baud with Tera Term, I can reset the G80 and see:
ÿG80
Version: 4.3.8.1
Debug: COM1
LCD: 0x0
.NetMF v4.3.1.0
G80, Build Date:
Mar 28 2016 08:14:04
ARM Compiler version 410713
TinyCLR (Build 4.3.1.0)
Starting…
Created EE.
Started Hardware.
MSdbgV1R¨½ cWCreate TS.
Loading start at 80826d4, end 80a8660
Assembly: mscorlib (4.3.1.0) Assembly: Microsoft.SPOT.Native (4.3.1.0) Assembly: Microsoft.SPOT.Hardware (4.3.1.0) Assembly: Microsoft.SPOT.Graphics (4.3.1.0) Assembly: Microsoft.SPOT.TinyCore (4.3.1.0) Assembly: Microsoft.SPOT.IO (4.3.1.0) Assembly: System.IO (4.3.1.0) Assembly: Microsoft.SPOT.Hardware.Usb (4.3.1.0) Assembly: Microsoft.SPOT.Hardware.SerialPort (4.3.1.0) Assembly: Microsoft.SPOT.Hardware.PWM (4.3.1.0) Loading Deployment Assemblies.
Attaching deployed file.
.
.
. 
So the G80 is working, pulling MODE low is working, the virtual COM port is working, the USB cable is working, the FTDI chip is working, etc. I think I’ve narrowed it down to FEZ Config / MFDeploy not working.