I realized that there was a faster way to do the ending for this level so I did some runs and went for it. I ended up optimizing this level more throughout my session and I finally got this run.

I stopped picking up the Desert Eagle, as the Beretta shoots faster, so it is better for killing the enemy at the bottom of the Control room stairs and the enemy holding the transit worker hostage. I skip killing the enemy with the shotgun at the top of the Control room stairs and I kill him when I go back up while waiting for the transit worker. This lets you take better lines, which is a slight optimization.

The part of this level after the train cutscene ends is where most of the time was saved off of my last run. You can jump up higher on the broken barrier and walk off it, which saves time. I also hit the superjump at the end of this run, which I think is ever so slightly faster than walking up the stairs if you land right at the door like I did in this run.