For the Galaxy S3, there's also a "no trip root" thread where you simply flash a root-injected TouchWhiz, which I used, and as long as you never flash anything non-Samsung in ODIN, you'll never trip the flash counter flag (which can be reset with TriangleAway anyway, unlike the KNOX flag afaik). But, once rooted, you don't need ODIN, and flashing TWRP recovery via the GooManager app (or dd'ing the img over the recovery partition) doesn't trip the flag, nor does subsequent ROM flashes from recovery over the system partition.
Is it the same situation here, or is the KNOX flag different, in that it will always get tripped as soon as it sees an unsigned partition on bootup?
Primary Phone: Note3 (SM-N900T); ROM: CyanogenMod 11 (KitKat 4.4.*); kernel: Stock @ 2.3GHz; misc: Incipio DualPro; 64GB class10 microSDXC
Other devices: Nexus 10 (stock), Moto X (GSM, unlocked & rooted)
SGS1 Captivate (SGH-i897) (internal flash died), SGS3 (SGH-i747), Nexus 7 (2012), Kindle Fire (otter), OG Galaxy Tab 7, ...)