Why is 'dukkha' included in one of the three marks of existence? In this link and this link the Buddha says that &quot;there is stress&quot; (or suffering or whatever your preferred translation of dukkha is). The Buddha does not say that suffering (dukkha) is inherent or an innate characteristic of existence.
According to the Second Noble Truth, this dukkha is caused by desire or craving.
So dukkha has a cause. That cause can be removed. It's not that existence is made up of dukkha.
I understand Annicca (impermanence) and Annatta (not-self) can be said to be 'marks of existence' i.e. existence is characterized by them. But I don't understand how dukkha is a mark of existence.
It is true that under certain circumstances humans feel dukkha but there is also joy, happiness, love etc. Dukkha is not a permanent building block of human existence. Annicca and Annata are permanent or basic building blocks.
So my question is, why is dukkha said to be a 'mark' of samsaric realm or material existence?
The teachings of the Buddha are not metaphysics. They do not describe the ontology or nature of things.
The teachings of the Buddha serve one purpose only - freedom from suffering. It's purpose is soteriological, not ontological.
In &quot;Anicca Vata Sankhara&quot;, Ven. Bodhi comments:

The most important fact to understand about sankharas, as
conditioned formations, is that they are all impermanent:
&quot;Impermanent, alas, are formations.&quot; They are impermanent not only in
the sense that in their gross manifestations they will eventually come
to an end, but even more pointedly because at the subtle, subliminal
level they are constantly undergoing rise and fall, forever coming
into being and then, in a split second, breaking up and perishing:
&quot;Their very nature is to arise and vanish.&quot; For this reason the
Buddha declares that all sankharas are suffering (sabbe sankhara
dukkha) — suffering, however, not because they are all actually
painful and stressful, but because they are stamped with the mark of
transience. &quot;Having arisen they then cease,&quot; and because they all
cease they cannot provide stable happiness and security.

First we have the first noble truth that tells us that there is suffering or dukkha. This is explained in this answer.
Next, we see - sabbe sankhara anicca.
This mark of existence states that all conditioned and compounded things (both mental and physical) are impermanent.
So what? What is the connection to you?
Next, we see - sabbe sankhara dukkha.
This mark of existence states that because all conditioned and compounded things (both mental and physical) are impermanent, therefore they are a source of suffering or unsatisfactoriness, because &quot;they cannot provide stable happiness and security.&quot; They are connected in this way.
These two marks of existence are there to show the connection from all conditioned and compounded things to the first noble truth of dukkha. In particular, they show the connection of the impermanence of the five aggregates (which are conditioned and compounded) to dukkha.
It's not there to explain the nature of reality. It's there as part of the narrative to explain the four noble truths.
The three marks of existence are mainly about YOUR existence. The marks of existence of a chair or table is unimportant.