Sonic Forces is the second game where time is mentionned. Infinite even states that Sonic defeated Eggman for "decades", and yet, nobody gets old. I'd say the Sonic X consequences reflect how time runs in the original video game series (since it is derived from it). Eggman's place into Sonic's world might have "stopped" time, as well as Sonic's place on Earth "could" have done the same.
How to say? Jackal Squad Captain × Phantom Ruby = Infinite.
I'd say he has become "something" which is not the Jackal Squad captain himself, rather than a person in a general term. Let's just say that the Phantom Ruby transform him into a supernatural "tool", which even Dr. Eggman uses for his Death Egg Robot, in the same way how he uses Metal Sonic and his other creations as "toys".