The only problem is this is a universe where they take the capacity to mess with people's minds seriously. Like it says in the Universe Info, the native telepaths in this world are usually forced to wear a mark showing they're telepaths due to its capacity to be a abused. Even if PCs can potentially avoid that, bare minumum, Legion leadership would likely make it clear to the team that a team member has that power.

Also, if it's kept secret by the Legion leaders, then if it gets exposed down the line, there will inevitably be a character that's going to be mad a power capable of such abuse was kept secret. That turns a convenient structure for handwaving things to the mods having to run damage control and play out conflicts with the Legion leadership over keeping secrets.

We're really trying to avoid that because the structures in place around the PCs to support them in being Legionnaires are vital for handwaving things and introducing conflict between the characters and that structure runs the risk of dismantling the thing that allows the game to even function smoothly. We'd prefer any conflict with authority figures to be directed at the villainous authority figures.

So in this case, we can only really allow that to remain a secret if they don't pick up on it in the first place. Going with the leadership just keeping it secret presents a little too much of an opportunity for "How could you keep secrets like that from us?!" down the line, especially if you go in certain directions with how he uses the powers. That being the case, you can absolutely have every medical scan miss it and just have it be a weird quirk that it's hard to pick up. We're willing to allow that for players in general if they want to play around with some secrecy around the characters' powers.

Would that potentially work for you?