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The following interpretations of 'metaphysical guilt', don't explain how 'metaphysical' in 'metaphysical guilt' connects with the meaning of 'metaphysics' as the fundamental nature of reality.

Source: Understanding Evil: An Interdisciplinary Approach, edited by Margaret Sönser Breen. p. 112 Middle

  Responsibility under these circumstances seems initially to fall within Jaspers' category of metaphysical guilt: the guilt we all share in allowing bad things to happen, in failing to help others, in taking actions that may harm others in some way, and in continuing with our ordinary lives when we know that too many others are utterly miserable and that sometimes their misery supports our own lives.23

Source: Nahshon Perez. Freedom from Past Injustices. p. 94 Middle

  Karl Jaspers, in his short essay, suggested distinguishing between four concepts of guilt: criminal guilt, political guilt, moral guilt, and metaphysical guilt.95 Jaspers briefly summarizes the four concepts as follows: [...] Lastly, metaphysical guilt is connected to one's status as a human being, which connects her or him to all other human beings. This connection makes him or her "co-responsible for every wrong and every injustice in the world, especially for crimes committed in his presence or with his knowledge.96 The relevant judgment of this guilt is with God alone. Note that Jaspers here emphasizes "human being" (rather than a citizen or a member of a specific community), and " God," as the judge, a notion which is inten- tionally far removed from individuals judging each other.

Source: Christopher J. Thornhill. Karl Jaspers: Politics and Metaphysics. p. 176 Top

  It can thus be seen that Jaspers' concept of metaphysical guilt is closely related to his transcendent(al) interpretation of cultural and political traditions. Metaphysical guilt, he argues, is a guilt which results from actions which negate the transcendent(al) (metaphysical) qualities which inhere in human tradition — in this instance, the tradition of German culture. All Germans are guilty, Jaspers explains, because all Germans are the inheritors of German culture and this culture has been betrayed by the millionfold murder of Jewish people. The meta- physical guilt of Germans, however, derives only secondarily from the actual concrete fact of genocide: it arises primarily from the fact that the transcenden- tally human possibilities of the German tradition have been catastrophically by German people.34 Humanity (here, the humanity of Germans) becomes metaphysically guilty, therefore, wherever it wilfully refuses to recognize and be guided by the transcendent(al) ideas to which it has access in its (German) traditions and cultural forms.

I don't quote this interpretation; its author has only a BSc in Computer Science.

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    It is "metaphysical" in the sense that the guilt does not result from breaking social norms laid down by law, morality or politics (or even religion, presumably), it is rather inherent in metaphysical "norms" of human condition, "transcendent(al) (metaphysical) qualities which inhere in human tradition", as Thornhill puts it.
    – Conifold
    Commented Mar 22, 2020 at 22:14

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Schopenhauer explains altruism as the 'breakthrough of a metaphysical truth' where the truth is the fundamental shared identity of sentient beings. Thus when we do not behave altruistically we are liable to 'metaphysical guilt', or guilt that arises from denying or ignoring our fundamental nature.

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To expand on Conifold's brief but accurate answer, you first have to understand that Karl Jaspers is closely associated with existentialism, and strains against some notions of the positivist tradition that seeks to settle metaphysics (if not eliminate it completely like the logical positivists and empiricists) in a place where objective sensory impressions and human reason exist as disembodied universals. Humanists often bridle under the notion that subjective experience and human values can be reduced to scientific, mathematical, and logical principles. Jaspers was a humanist who is often seen as an extension of the existentialist tradition. To wit:

Most commentators associate Jaspers with the philosophy of existentialism, in part because he draws largely upon the existentialist roots of Nietzsche and Kierkegaard, and in part because the theme of individual freedom permeates his work. In Philosophy (3 vols, 1932), Jaspers gave his view of the history of philosophy and introduced his major themes. Beginning with modern science and empiricism, Jaspers points out that as we question reality, we confront borders that an empirical (or scientific) method simply cannot transcend. At this point, the individual faces a choice: sink into despair and resignation, or take a leap of faith toward what Jaspers calls Transcendence. In making this leap, individuals confront their own limitless freedom, which Jaspers calls Existenz, and can finally experience authentic existence.

Also...

He valued humanism and cosmopolitanism and, influenced by Immanuel Kant, advocated an international federation of states with shared constitutions, laws, and international courts.

So, in the humanist and existentialist traditions, there is a metaphysical presumption that is highly altruistic in nature. That all of us are our brothers' keepers. That's a very normative philosophical presumption. Unlike the law, particularly with punishment often attached, morality which is often an extended theoretical system based on reason by which one can arrive at the conclusion that the greatest good might outweigh the good of an individual, or politics (and thereby religion) where often what is good is what is politically expedient, Jaspers like Carl Rogers, A. Maslow, Rollo May, or J.P. Sartre, believes that the individual automatically bears responsibility for the welfare of any other person by virtue of being a human being involved in the collective enterprise of social existence, even when going through Self-Actualization or the pursuit of the Authentic Self. The existentially aware being cannot choose not to be responsible for his fellow human because it comes logically prior to the philosophy itself. German are social creatures, and hence Germans are responsible for Germans since they have access to the transcendentals of German culture.

And this then is why the term is applicable; for what is presumed to be true as first principles in the edifice of a theory must by definition spring from the nature of reality itself. Thus it is a metaphysical presupposition that a human is responsible for all men, and not a conclusion drawn from math, science, or logic, but because men have knowledge of the transcendentals such as goodness which exist a priori to man and society.

At least, that's how I see it.

EDIT: I think the argument goes that good is a transcendental that humans have access to (a metaphysical precept) and that moving forward with existential awareness embodies a simple principle: that for any person who suffers for whom you choose not to do something to prevent or assuage, you are in fact neglecting that person. This is not to say that it is possible to do something for everyone, for that's not possible, but acknowledging that it is not possible in all instances simultaneously doesn't absolve you from the fact that you choose not to help everyone in any specific instance.

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