Without diving into complex semantics, let's simplify the questions:
A. does the severity of an act depend on its substantivity (actus reus), or intention (mens rea).
B. why some acts that have no apparent moral implications may be considered penal sins.
To put it even more simply: how do we quanity the vice and virtue of an act, and why.
First of all we need to clarify - whom are we asking?
Are we asking the opinion of secular legal systems, our personal opinion, the opinion of other religions - or, the opinion of Judaism?
Then, before asking "how is that even possible to say so", let's first understand what exactly is being said, and address the personal dissonance later on.
Assuming that we are curious to know the opinion of Judaism, we may not base the answer on any other apriori pressumptions other the ones that Judaism itself provides us.
So: how do we quantify vice and virtue?
Looking at the Jewish penal code we can observe that every act consists of a combination of substantivity (actus reus) and intention (mens rea).
Some laws hold more "substantive" value, e.g, doing Melacha on Shabbath is worse than murder, which is worse than eating pork, which is worse than not wearing Tefillin, which is worse than breaching דרבנן laws, which is worse than putting your shoes on in the wrong order, assuming the same level of intention.
Likewise the intentive value can either nulify the vice ("מתעסק") or increase it (מזיד לתיאבון, מזיד להכעיס).
However, we have to keep in mind that this is only from a legal point of view, that can only be based on objective measurements.
The actual "amount" of vice and virtue depends on additional variables, such as environment, knowledge (or lack thereof), spiritual level, mental state, etc.
And now the second part: why are some acts virtuous or vicious acc. to Judaism?
There are two main approaches to that question - instrumental and intrinsic.
Rambam in Moreh Nevuchim explains man's purpose as understanding the truth, and the commandments serve as essential instruments to achieving that goal.
Some Hassidic writers (e.g Yesod Ha'Avoda) view man's purpose as developing love or reverence to HaShem, and commandments as instrumental.
So morality, good and evil, are all based on the question - does it bring us closer to our purpose, or move us further?
Nefesh HaChaim on the other hand point out the "opus operatum" nature of the commandments. Just by performing a prescribed act, with the right intention, you automatically gain virtue and have spiritual influence on the world / other realms, and the physical, emotional, mental effect of the act is of second importance. Thus, it doesn't matter at all how you feel toward tying your shoes, but rather the mystic effect thereof.
As Raschar Hirsch in 19 letters points out, both schools of thought have their weaknesses:
how does a certain purpose (even if not arbitrary), like love or attaining knowledge, imply 613 commandments? What does it have to do with tying shoes? But any attempt to "cut off" any commandment, even if rationally appealing, could be called Christianity, Reform, but not Judaism.
where in the Torah does it say that commandments are mystic amulets, that have nothing to do with actual life?
He himself offers another approach, a more "holistic" idea of virtue, that is explaining how the commandments are not merely mystic, but actually humane and moral, and not only opus operatum, but have the purpose of bringing humanity to a virtuous path.
So as for the question why, you won't have a straightforward answer. Arguably all of the above are true in a way, but you might get a fuller understanding by studying Tanakh / Talmud / Midrash / Zohar.
Lastly we shall address the personal dissonnance.
The dissonnace is a contradiction between our view and the view we are looking into. The question "how is that possible" is merely an emotional expression, but we already know the dissonnance exists.
So, knowing the opinion of Judaism, instead of asking "how is that possible", let's ask ourselves, what are is our own opinion?
Do we have conservative or liberal predispositions? Do we value equality, freedom, feminism, rationalism, or nationalism, romanticism, traditions?
What is our own idea of vice and virtue? Do acts have intrinsic value, or instrumental value? And if we don't have a clear sense of good and bad, how can we judge those who do?
Next, how did we acquire such views? Is our opinion trustworthy?
Contemporary western socities value freedom.
Now, if freedom is thought to have intrinsic value, we might inquire, where from did it acquire such value? Arbitration?
If it has instrumental value, then what its purpose? Achieving happiness? Then, where did happiness acquire its value? Arbitration?
Marcus Aurelius in Meditations 2 10 quotes Theophraktus, who says that crimes committed out of passion are more shameful than crimes committed out of anger, and provides his reasoning for it. But how is he so sure?
Tying shoes correctly surely doesn't have any intrinsic value in the eyes of western morality, and doesn't serve as an instrument to achieve any of its goals (well-being, pleasure, whatever that is), and thus meaningless.
But in the eyes of Judaism - isn't it a reminder to remember HaShem whenever you go outside for your business? Isn't it an ancient tradition of the nation of Israel? Doesn't it have some mystic value? And by favouring the own opinion - isn't it equal to saying that one trusts and serves only his intuition, and is not willing to bow down before HaShem's Will?