Hello VagalTone
There seems to be some misunderstanding about Karma and the concept of Karma as used in Buddhism (sorry, do not know anything about Hinduism).
Karma is not faith based, since the concept of karma in buddhism basically means some action(s) will lead to some result(s). Without the force of Karma, the world and its beings would not exist.
Therefore the goal of all buddhist traditions is to cut the root of all suffering, meaning cutting the root of that which produces karma and afflictive emotions (which in itself produces more karma), which is a active misconception of how things really are (called Ignorance in buddhist terms).
All actions based on a dualist frame of mind (basically meaning that you are not enlightened), will produce seeds in the consciousness of that being. Depending on what tradition of buddhism, there are different explanations on where and how these seeds are stored.
Your use of the term substrate consciousness, is a term used in Mahamudra and Dzogchen, meaning the alaya-vijnana or the 8:th consciousness.
From the point of view of these traditions, all sentient beings are mentally disturbed

some more, some less, but still mentally disturbed in that sense that we believe our self and the outer world to exist in a way that is mistaken with how it really is.
So if a mentally disturbed person would not accumulate karma for his or her action, neither would a "sane" person do.
The only different between the so called sane and mentally disturbed person is the force of this Karma.
The force of the accumulated karma depends on the strength of the intention behind the act (and some other factors, but let us leave that aside), so if you are very clear on what your intentions are when performing the act, the force of karma will be stronger, then if you perform the act not know it.
Lets take the example of killing someone:
If you are very clear in your intention and know what you are doing, this will leave a very powerful imprint on your mind, what buddhism would call Karma. The logic behind this is that if you perform an act over and over, with a clear knowing of what you are doing, it will more easily create a habitual behavior pattern likely to be repeated in the future (the seed of karma stored subconscious), meaning that the force of karma is stronger then if you happened to be driving down the road an by accident kill someone.
You would still accumulate the karma of killing someone if you just by accident happened to kill them while driving down the road, but the force of this seed will not be as strong, since there were no intention behind it, hence the karma accumulated would not be as strong as with the person above.
Once again, the logic behind it is that ALL acts, performed by someone knowing what they do or not, will generate karma since all actions, thoughts, feelings and so on, will leave an imprint on the mind. These imprints will effect (not decide) how you interprets the world around you, leading to emotions (this I want, this I do not want), which leads to actions (lets get the hell out of here!), which once again leads to accumulation of karma, which then solidifies how you interprets and relate to the world.
This is why all beings not enlightened are said to be trapped in Samsara, Samsara meaning an ever revolving wheel with no end driven on by the power of Karma.
Also, the question of free will is of utmost importance in Buddhism.
Karma is not seen as some "Law" that is inescapable and imposed by a moral just or unjust "Universe", but the natural consequence of the more you perform an act, good or bad, the easier it is to form a habitual pattern about this behavior, something we try to use at our advantage when practicing Lucid Dreaming.
This means that Karma is something that you can clear away or increase depending on your behavior. Preferable you like to increase your positive Karma (called merit in Buddhism) like compassion, generosity and so on, and decrease your negative Karma like pride, aggressiveness and so on. many practices in Mahamudra and Dzogchen are meant to clear the substrate consciousness from all seeds (habitual patterns) and therefore clearing away all automatic responses when an emotion comes.
This is free will! You do not react any longer like a trained monkey. When an emotion comes, there are no pre-set karmic behavioral patterns to trigger and instead you chose how to react in this situation.
In other words, you are no longer on autopilot, and therefore chose what karma to accumulate (good or bad) or at the highest level, accumulate no karma what so ever (but this is a bother discussion

and can break free from Samsara.
Sorry about my long replay……
Carl Wallmark
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