You have to wonder what the heck people who don't have access to Morph Ball technology are using those tunnels for. The Luminoth I guess have the whole "Kinetic Orb" excuse, but why do Chozo and Space Pirates insist on having tunnels too small for them to use but the perfect size for the Morph Ball?

Not to mention the fact that half the time you actually have to fix the pirate base to proceed. Have the pirates ever heard of maintenance?

Clearly, Alien bathrooms are horizontal.