The useful OOB and time saves found so far are at the following points on the 57:44 run:

7:15: clipping through lift to save waiting for it; 8:50: shooting the ladder down and starting the climb before the phone conversation starts, to avoid waiting for the conversation to end beforehand (and restarting at the top of the ladder to skip the rest of the conversation). 10:26: clipping through cutscene trigger and hugging the wall around to the platform, then clipping through the barrier and beyond the gate - this saves 2-3 minutes at least I reckon. 11:56: restart saves a few seconds. 12:19: hugging barrier and restarting avoids the lengthy cutscene with the doctor. 13:05: restart saves fighting the mobs on the stairs. 18:28: clipping through the lift avoids a mini boss fight and saves a lot of time. 23:03: restart saves a few seconds. 28:52: this area can be run through without killing the mobs and then quitting and reloading (not restarting, as the cloaked guy does not spawn otherwise) once the next checkpoint is reached. 32:18: restart saves a few seconds. 35:42: clipping through the right hand side of the gate and then restarting skips a big section. 36:55: a barrier can be rolled through which saves a little time. 41:15: after killing the first round of mobs in this area, you can clip through a small gap to the right of the gate, which saves a long standoff and a lot of time. 51:00: walking up the left edge of the stairs here allows you to slip over the barricade and saves a fight on the platform and a cutscene. Note that you have to walk over to the stairs on the other side to trigger the next checkpoint.