In the spirit of the above article, I thought it would be helpful to list as a reference the possible ways a speedrun mod could reduce the run time and allow players to focus on grinding the challenging sections (there could be a category for it maybe in category extensions). These are all currently achievable with existing modding tools and most are implemented in Kitty: Isolation mod. Time saves stated are approximate.
M1 - (2:35) Able to run to the bridge immediately. A flare and a medkit blueprint would be available on Taylor's table to compensate for not finding them in M2. Mission ends automatically upon entering the bridge.
M2 - (15:00) The entire mission is skipped. The only danger sacrificed is getting past the humans near the end. It can be assumed you would have used a flare for this, hence why only one flare in M1.
M3 - You automatically start the mission with the flashlight and maintenance jack
M5 - (0:35) Dialogue with Kuhlman is shortened so doors open sooner
M8 - (2:25) Brace is removed from the elevator and the elevator is already open. The transit to Solomons loads you directly into the start of M10 (facing Marlow as he concludes his story)
M9 - (10:57) The entire mission is skipped
M11 - (0:42) Torch panel door is removed near start of mission, robot vent is open without robot
M13 - (0:52) Code door near entrance is already open and vent hack isn't required for Apollo
M15 - (2:26) Anesidora doors no longer need code/hacking/gens, some dialogue is cut
M16 - (3:00) Shortened dialogue and being able to run during spacewalk
M18 - (0:58) Able to run during spacewalk
M19 - (0:10) Able to run in spacesuit
Total (39:40) - Potentially making for a sub 2 hours NMG run. Some other shortcuts are possible with the mod, but I've tried to only include those that wouldn't alter or affect any challenging parts of the vanilla game.