One of the ship's data entries explains that the ship's reactors are based on Dr. Kirk's thrid energy research from the first game. Also, the spaceship escapes the explosion just like the chopper in the first game.
The computer called Mother first appears in Dino Stalker and then later in Dino Crisis 3. Furthermore, the idea of genetically modified dinosaurs is introduced here in Dino Stalker first. Also, Dino Stalker very loosely sets up the story of Dino Crsis 3.