1. Not when it's the leader doing the infiltrating and reporting information to the subordinate so he could pass it on. Maybe you also missed the part where Koby reported to Drake what he was doing as well. There's no law in a military unit "leaders don't relay information to subordinates".
2nd. Koby does have a position, he's a rear admiral in the marine HQ (which Oda mentions) aka the same rank Drake was when he went undercover. However, within the SWORD Koby is simply a member of it. Nothing sus about it.
3rd. You called them an organization, I corrected you on it. They're not an organization in the world of OP, they're a division under the Marine HQ, which you now corrected in your reply. And glad you accepted the "Coby's division" being headcanon as well.
Terrible example by comparing the Cipher Pol as a whole to the SWORD.
Cipher Pols 1-9 are collective organization akin to the Marines , Warlords, and the other two mentioned here. All 5 organizations of the World Government reporting directly to the Commander -in - Chief Kong & The Gorosei. SWORD is a division within one of those 5 organizations.
CP 0 are a seperate organization like the Marines, Warlords, etc.. that's directly under the Gorosei themselves. Which again is nothing like the SWORD when it comes to structure. SWORD is 1 specific special forces unit.
But as I said, yes there is a SWORD Vs CP0 being built up which Koby will be part of, and the one who's at the core of it is Drake, the captain of SWORD.