This would mean that if you want you can wear any armour that can be considered "light" rather than specifically leather level armour. This change would allow modded armour to work a little better. This is just a slight tweak but it would greatly increase synergy with other mods.

The "Light armor" assessment is already based on damage reduction/absorption level.
Specifically:

• for simple armors (derived from vanilla ItemArmor), the chest plate version of the material should be lower than or equal to 4 in terms of damage reduction
• for advanced armors (implementing the ISpecialArmor interface), the chest plate version of the material should be less than or equal to 0.16 in terms of damage absorption from a cactus.

I did fix the code structure back in July 2019, but the intended behavior didn't change since at least Sept 2016. I'm not really fluent with damage calculation, so I can't tell if the scaling is correct or too lax/restrictive.

I should probably clarify what I meant since I may have made a misunderstanding. What I mean is that instead at looking at the individual armour pieces and checking if it is the same "grade" as leather, it could instead check if you have 7 or less armour points total (the total amount when in full leather).
This could be done so that you can still wear, say, a chestplate that provides 6 armour points and the threat matrix would still work but wearing boots that give 2 more points would stop threat matrix from working.
I'll be honest, I didn't even consider how this change would affect armour that used different armour calculation so I understand how it would probably be more complicated than I thought.
If you would still be willing to implement my suggestion, this could just be a toggle in the configs that switches between the older version and this version of how threat matrix works.

Let's focus on the lore first... The threat matrix is about boosting your reflexes to move super fast to dodge an attack. That implies that your body isn't encumbered. Having an heavy chest plate with no other armor would still impact your speed to react.
Now, what I find a bit weird is that with no armor you've 65% chance to dodge and it rises to 70% with a light armor. For me, it should be the other way around, and the 70% doesn't justify getting that upgrade in mid/late game when you can do implants. I feel a 90+% chance to dodge would make more sense while still taking full damages from area/explosion and potion effects. That would give more incentive to get a Threat matrix implant while keeping it balanced. This would also make mobs much harder to kill when they have that implant, so adjustments might be required.

That can work too. It seems like the mod in general just needs a little more transparency in some places if this is the case, not just with the threat matrix.
Other than that I think some tweaks or a revision of the threat matrix could do the augment some good, though this might mean some other augments might end up being out of balance or its benefit might be too good compared to other augments.
I think this thread can be considered resolved? I can't think of any thing else to say about the threat matrix.