Preferences->Fonts->Active Fonts
To only deal with <Active Fonts>, uncheck all of the boxes except <Active Fonts>. By doing this FlightCheck will only flag a font as missing if it is inactive.
Important Note - Even though the other Paths are unchecked, when you preflight a job, FlightCheck currently still scans through the unchecked paths for System:Library:Fonts, Library:Fonts and Users:yourfolder:Library:Fonts.