Here is a pic of my FB config when 12V regulated is powering the FB:
You can see in this pic that the FAN is enabled and the there is no LED showing the dig output is enabled. That port is always outputting ~11.2V when a regulated 12V is supplied to the FB.
Here is my config when USB is powering the pics and 12V for DO's:
The DO led is lighting up, and is outputting ~11.37V
You said it wouldn't be a good practice to power the FB with 12v and USB but don't they share the same ground (in my CarPC they do but not my test setup)?