This game's been out for nearly three years on Steam, with the true ending having always been an unsolvable enigma. With the introduction of the Xbox One version, we learned that it was indeed possible, because of the always online achievements system. Recently, someone on Steam had mentioned having gone code diving and found that the true ending was somehow tied to oxygen and energy. And now, one video later, we have the solution. You literally just need to have a high enough energy and oxygen value. Thanks to marcoferre117 for finding the video:
Now, the video has you starting the countdown, then grabbing the energy pickup and oxygen, and then grabbing the canister post-countdown. I tested to confirm you don't even need to do that. Grab the outer three green switches, swim to the bottom to grab the oxygen and energy, then swim back up to the fourth switch and canister, hit the switch, and grab the canister. Terribly easy.
Now, I doubt this'll be an issue for anyone that's able to get far enough, but if you find that you aren't getting the true ending despite doing it as such, then your initial values of energy/oxygen might be too low to start. So you may need to restart a few levels back and play forward again to level 38 to hopefully have a better oxygen and energy.
Edit: Seems like it's not all rainbows and sunshine all around - the Steam version still seems incapable of popping the achievement - and even if it was, there's an absent-from-consoles no death run achievement that doesn't unlock either. PS4 true ending does seemingly work fine, one guy over on TrueTrophies has it... yet there's an achievement on PS4 that nobody has yet that could possibly be glitched.