My thought was mostly just a one-time event at some point in the game and variable epilogue flavor text if he went with her into the program or not. Nothing too robust. It's something I realized in passing might be an interesting touch, but we can just as easily write it out as the player already have missed a submission deadline or whatever.
Unique interactions based on if the S-Link has already been cleared might be do-able, they'd certainly have to exist for sex scenes to function.
After finishing incorporating Twilight's story into the game, I'll see what I can do system-wise to enable this.