I think the difference is that this is a known condition for Boydy. There's a really high chance he'll cop another head knock at the back end of this season and the Roosters will get another 350k for next year's cap.
If there's a clause that this is a one time exemption for this particular injury then I see no big deal.
The injury occurred when playing at rep level, so it will only apply on this occasion. It does not matter whether there was any pre-existing condition, otherwise I doubt Foran's request would have been granted. To be eligible the player has to be out for at least 12 weeks, but the maximum compensation is $350,000 regardless of what actual salary the injured player was on, and can only be used for paying a "like for like" replacement (e.g. as Cordner is a forward, you could not use the money to sign a back or half). Further the money cannot be used to top up the contracts of other players.
For a club to get similar salary cap relief, a player would have to get injured whilst on rep duty and be out for 12 weeks or more.
Also remember, it is not automatic, the club has to provide evidence for their claim to the NRL for it to consider (as happened with Kieran Foran and Josh Hodgson).