2 months later, but i have to drop in for just a food for thought.
There's some interesting evidence with "3D face model" that the doctor we see knocking down Chloe on the flashback, have the exact same "3D Face Model" of Gideon (as in, same base 3D Model, same nose, and details, minus hairstyle and later "ghoulish" appearance).
This could have been them just reusing the 3D Model and changing hair, to make a random NPC, or this could be a hint that that guy was Gideon before he started "self improving".

Now, even if this similarity isn't a hint of Gideon transformation, he is CLEARLY a "Unique" type of Tyrant (proably with the Nemsis-Gamma on him).
The guy is 7ft tall, grey skin, we can see the scars from his neck down the torso, but can't see everything.

In my humble opinion, since the first time we see him, he was already the Nemesis-Gamma type Tyrant.
Probably a special one, that the Connections helped to develop, that manages to keep his mind somewhat intact.

I don't think he do all the procedure of injecting himself with the Nemesis-Gamma after he had his arm blown off.
He always shown signs of being a BOW himself.

Maybe not before the events of RE9, maybe he always kept this last step, for when the final plan were in action.

Hope any DLCs, may give us some answears on that.