You can customize Preferences in Markzware‘s preflight solution, FlightCheck, to only deal with <Active Fonts>. Here is how prepress professionals can be alerted to inactive fonts that are missing:

FlightCheck 7.5 Mac Preferences: Active Fonts

In FlightCheck‘s Preferences, under the Fonts tab, there is an <Active Fonts> option.
To only deal with <Active Fonts>, uncheck all of the boxes, except <Active Fonts>.
FlightCheck will then only flag a font as missing, if it is inactive.

Important Note:
Even though the other Paths are unchecked, when you preflight a print job,
FlightCheck scans through the unchecked paths for:

• System:Library:Fonts, Library:Fonts
• Users:yourfolder:Library:Fonts

Collect Files, Package Fonts and More with Preflight Software, FlightCheck

For more information on Markzware’s pre press software to check digital files for print quality control, see the FlightCheck page. For more desktop publishing (DTP) and printing solutions, please see the Markzware Products page.

FlightCheck 7.5 Mac Preferences: Active Fonts