Level and exploration design are much more specific than "because you shoot things in space." In fact, if I were to focus on themes and what you can do, then Dark Souls and Metroid Prime wouldn't be similar at all. Instead I chose to focus on the actual design of the games. Both games have corrider-focused level design where each hub is connected to all other hubs in a spider-like pattern. Both games tell their lore through the world and gameplay, rather than through cinematic cutscenes. Both games have a boss at the end of each hub area. Both games take a balance of linearity and non-linearty. Both games have a strong emphasis on exploration. Both games are part of the Metrovania subgenre of the Action-Adventure genre. So on and so forth.
Many game ESP from the Gamecube era had a similar map layout because of the limits of the era. Metroid and Souls could not be more different of gameplay styles. Big whoop both are corridors. Still nothing alike and Metroid should never be souls like ever. Not even take a single note from it. You have surface level comparisons but they are still woefully different games.