Here is what I found that differs...
RegularFactor#0 was stated as being a fatigue hit for being placed into the compartment when surfaced. I have found by isolating and moving a way different setting around that it actually applies ANYTIME - not just when surfaced. Of course you can only get to some when surface, but the observation remains true. You can also configure a fatigue hit when moving into rest quarters - imagine total collapse after a grueling shift.
RegularFactor#1 was not agreed upon, it was suggested by some that it was the submerged version of RegularFactor#0, and there is support for the submerged part due to the fact that none of the topside compartments are enumerated. However, I confirmed that it is NOT a submerged hit for moving into the compartment - those hits are absolutely controled by #0. It also has nothing to do with silent running. No idea for now.
Whatever it is, I am going to play with the settings below for a while. Sooner or later the trigger will occur and I will have a fatigue bomb that will wipe out everyone but Damage Control and Aft Torps. Hopefully I will at least have a clue what caused it

If someone else wants to booby trap but exclude different compartments it may lead to a discovery sooner. It could be a damaged compartment modifer or something like that. Knowing it would likely be useful.
;RegularFactor#1 = unknown - waiting...
; ;Twr
RegularFactor11=0.4;R/S
RegularFactor21=0.4;Cmd
RegularFactor31=0.4;Die
RegularFactor41=0.4;Ele
RegularFactor51=0.4;FwT
; ;FwQ
; ;AfQ
RegularFactor81=0.00004;AfT
: ;DG
: ;AA
RegularFactor111=.00004;D/C ; very minor hit