At no point is it stated this ability applies only to space and matter, or is limited to functioning in the same direction as the arrow of time. Thanks to the Von Braun's FTL drive, SHODAN can rewrite reality to her specifications.If you listen to the log in question she only ordered he be placed in the cryo unit to heal, that wasn't an order for the actual surgery.Either he was specifically placed under her authority somehow or Tri Op is such a Mega-Corp that she can order soldiers around. Yet a message bearing her name is enough to order a military soldier (Soldier G65434-2) to undergo brain surgery and cyber-implants. Janice Polito was a civilian doctor with Tri Optimum.

So then why are they readily available aboard the Von Braun? An audio log mentions that the 'R-grade cyber goodies' about to be installed in the player-character are illegal.The shotgun has been modified to work with the Hybrid's mutated limbs, rendering it unusable by the Soldier. So how was it shooting at you in the first place? Whenever you kill a shotgun-toting hybrid, the gun it's carrying is jammed.

System shock 2 hybrid