The very ending of Mark S going away with Helly R was beyond stupid of him.
I get that he doesn't want to "die". I get that he loves Helly R. What Mark S just did set himself up to be in Mark Scout's state of tragedy before Mark Scout the took the job at Lumon before that Mark S gets destroyed forever.
There was nowhere for Mark S and Helly R to escape on the Severed Floor. They will be found, and quickly. With Cold Harbor done, there is no need for Helly R to be on the Severed Floor so she will never return as soon as Mark S and Helly R are found and Helly R is dragged back to the elevator to become Helena Egan again. So Mark S loses her making Mark S lose the love of his life, just like Mark Scout did when he lost Gemma.
Here's where the real hell begins. The Mark Scout/Gemma + Mark S/Gemma's brain process was interrupted (destroyed?) by Mark Scout on the black elevator floor. Except...... there's nothing preventing Lumon from simply wiping Mark S's memory by creating a NEW Mark S Innie! They even said in the episode that 24 Gemma Innies had been created, one for each "file"/room. So they can easily create new Mark S innie, put him in MDR, and drag Gemma back down to the basement again and force her through another 25 rooms. A new Gemma Innie is created in each one, so if they can create 25 before, 50 doesn't seem to be an issue. As for Mark Scout, they'll keep him in a prison somewhere just like they did with Gemma. Mark Scout will have no memory as NEW Mark S Innie and Lumon still gets the exact outcome they want from the first time around. Mark S is an idiot.
Original Mark S lost the love of his life, erased his own existence, and doomed Gemma and Mark Scout to hell on Earth trapped for the rest of their lives in prisons.