Internally, the CTF variant just basically sets a property on the player who was in the pickup the radius that says they're carrying the flag. Then when that player is within their flag stand's radius it checks that property and performs that scoring logic from there. If I recall, this is also how Reach's CTF worked as well. Been a while since I looked it though.

I swapped the grifball with the flag in a Grifball variant and there wasn't even an option to pick up the flag when I disabled the Grifball 'automatic pickup' option, which hints to me that the flag object doesn't have any properties for picking it up, either automatically or by holding action.