Sorry I missed this one earlier... The CONFIG_FLAGS can be changed from QGC "Onboard Parameters" view by directly editing the line and then saving the changes. However QGC may reset this value when saving changes "normally" (from the main config UI), so it will need to be updated each time.
I've already added this option to the QGC code (GitHub) but it's waiting on the next release -- perhaps Angel's version already has it in there: viewtopic.php?f=23&t=4910#p37484
-Max