Glitch's cutter blade is different than other episodes; in this one, it is mounted on an arm instead of flush with Glitch. Given, it might be a different cutter, but it's triggered by the same words.

Endoporpoise

Since we learn in later episodes ("Infected", "Mousetrap") that Glitch and presumably all other Guardian keytools are at least semi-sentient and capable of improvising to suit the situation at hand, I see no problem with this.

Starship Alcatraz is the first game that shows Bob and Dot playing game roles that would normally be User roles, while the User plays a role that would more fitting a game sprite, like the other misshapen inmates Bob and Dot have to contend with.
What's the objective of the game? Escape? The User, minus his stolen card key boards a vessel or some other module jettisoned from the cell block, but that doesn't end the game. Retrieving the card key and deactivating the self-destruct is what ends the game.