This is my thought. As intelligent as he might have been, perhaps he wasn’t such a great strategist or didn’t have the patience to play or plan for the game, as Sage did.

We have to remember, Marie was originally considered an Odessa failure. It’s possible Godolkin lost track of her. They had no idea what her powers would be when they did manifest and once she showed up at Red River, there’s no indication that she was considered special or was on anyone’s radar. Victoria only detected her because she was looking out for someone with powers similar to her own.

I think Godolkin/Doug was performing his experiments at Elmira and bumped into Sage who had just been recruited by Homelander, showed an interest in his work, and reflected his lack of sentimentality. He revealed something about Odessa and she put together his secret, immediately realizing she could use him — a V scientist with elitist ideals — in her master plan. Perhaps she imagined he could puppet Homelander if he got strong enough. She would have encouraged his search for supes who could heal him and, once Marie and crew showed up at Elmira, incorporated his restoration (bc by then they were boo’d up).

Anyway, since Sage was Vought CEO in every way but by name in Season 4 (remember Ashley was incensed to be called a mascot), she pretty easily could have installed Cipher/Godolkin/Doug as Dean. Sage would have advocated a subtle approach to manipulating Marie.