the KSM module seems to be applying the melee bonus damage to base melee damage and negates bonus damage from perks.
Im running Mechatronic warfare, spark arsenal, pugilist class, brawn class, and haywire spark bit.
in troubleshooting the iconoclast class's brawn perk from the brawn SPARK mod, i noticed that melee damage without KSM was 14-16. with KSM it was 12.
this made me check the SPARK class from mechatronic, and the pugilist class.

Without KSM:
SPARK mechatronic (with concussive strike, assault servo perk, plated chassis):
strike was 10 damage.
this is correct: tier 2 base damage= 8 (+2 from assault perk) = 10
concussive strike (half damage) was 6.
correct: (half of 8=4, +2 assault)=6

Pugilist (with gutshot, and haymaker):
strike damage: 8
gutshot(reduced damage(*0.75): 6
correct: (8*0.75)=6
haymaker(50% increase): 12
correct: (8*0.5)+8=12

With KSM:
mechatronic: strike was 12
((8*0.6)+8=12) but it should be ((10*0.6)+10=16
concussive strike was 4 (KSM multiplier not being applied?)
should be: ((6*0.6)+6)=9

Pugilist: strike was 12
correct: ((8*0.6)+8=12)
gutshot: 9
correct: ((8*0.75)*0.6)+6=9
haymaker: 19
correct: (((8*0.5)+8)*0.6)+12=19

Thus, Pugilist class is the only one working correctly with KSM from my testing.