As per my reading from Wikipedia, the mukhya Upanishads discuss the philosophy of vedas. The seeds of advaita and vishishtadvaita philosophies are found in these upanishads as per my limited readings. Where in samhitas can we find a correlation of the verses in the Samhita and these propounded philosophies such as advaita and vishistadvaita? Also does the Mukhya upanishads make direct references to Samhitha verses in the exposition of their philosophies?
Where in samhitas can we find a correlation of the verses in the Samhita and these propounded philosophies such as advaita and vishistadvaita?
Yes, we can find seeds of the monistic philosophy in particular in Veda (SamhitAs) only.
As per philosophers like Sri Aurobindo etc the Atharva Veda is the 1st Hindu scripture that clearly indicates the origin of the monistic school of thought. Where the God and the human being (the Jiva) are not considered as completely separated. The Brahman or God has entered the body as stated in the following Mantra:
PrabhAjamAnAm harinim (1),
YashasA sam parivrutAm (2)
Puram hiranayayim (3),
BrahmA vivesha (4),
The Brahman entered (4), the resplendent, yellow, golden, unconquered city (1,3,5), that was surrounded with glory (yashasa) (2).
Atharva Veda 10.2.33
BTW, here the word "Pura", which means a "City", is referring to the human body. This becomes clear once we read the other associated Mantras.
Note that the human body is regarded as "a city with 9 gates"
Chandradhar Sharma gives many references in his book A Critical Survey of Indian Philosophy available here - https://archive.org/details/IndianPhilosophyACriticalSurvey on pages 16-17 he writes:
...So there is no question of crude monotheism also in the Vedas. Hence there is no development from polytheism through monotheism to monism, but only of monism from the first Mantra portion to the last Upanishadic portion.
Let us take some illustrations. 'The One Real, the wise declare as many' (Rgveda, I.164.46). 'Purusha is all this, all that was, and all that shall be (Ibid, X.90). 'The real essence of the gods is one' (Ibid., III.55). 'The same Real is worshiped as Uktha in the Rk, as Agni in the Yajuh and as Mahavrata in the Sama' (Aitareya Aranyaka, III. 2.3.12). 'Aditi, the Boundless, is the sky, the air, the mother, the father, the son, all the gods and all the men, all that is, all that was and all that shall be.' (Rgveda, I.89.10). 'He is the Custodian of the Rta (Truth), the binding Soul of the universe, the unity-in-difference in the cosmic and the moral order' (Ibid.,X.190.1)...'We make sacrifices to the ultimate Lord of the universe, who runs through every particle of this universe, the whole existence, and who is Blissful and Indescribable' (Ibid., X.121.1)...'There was neither Being nor non-Being, neither air nor sky, neither death nor immortality, neither night nor day; That one breathed calmly, self-sustained; nought else beyond lay' (Rgveda, X.129)...'He is immanent in all this creation and yet He transcends it' (Rgveda, X.90.3).
Read pages 13-18 for a better understanding of the relationship of the vedas and the upanishads.
This useful answer already mentioned some verses, I'm here quoting one direct verse from 1st Mandala of Rigveda which are found in 2 of 11 Mukhya Upanishads:
Riveda 1.164.20 = Mundaka Upanishad 3.1.1 = Shvetashvatar Upanishad 4.6
द्वा सुपर्णा सयुजा सखाया समानं वृक्षं परि षस्वजाते ।
तयोरन्यः पिप्पलं स्वाद्वत्त्यनश्नन्नन्यो अभि चाकशीति ॥
Philosophy of Veda: (Rigveda 1.164)
20 Two Birds with fair wings, knit with bonds of friendship, in the same sheltering tree have found a refuge. One of the twain eats the sweet Fig-tree's fruitage; the other eating not regardeth only.
21 Where those fine Birds hymn ceaselessly their portion of life eternal, and the sacred synods, There is the Universe's mighty Keeper, who, wise, hath entered into me the simple.
22 The, tree whereon the fine Birds eat the sweetness, where they all rest and procreate their offspring,— Upon its top they say the fig is luscious: none gaineth it who knoweth not the Father.
Philosophy of Upanishad (Mundaka 3.1.1 & Shvetashvatar 4):
IV-6: Two birds of beautiful plumage, who are inseparable friends, reside on the self-same tree. Of these, one eats the fruits of the tree with relish while the other looks on without eating.
IV-7: Sitting on the same tree the individual soul gets entangled and feels miserable, being deluded on account of his forgetting his divine nature. When he sees the other, the Lord of all, whom all devotees worship, and realizes that all greatness is His, then he is relieved of his misery.
The interpretation of this verse is key part in the philosophy of Vishishtadvaiata, though Advaita interpretation is also discussed here.
Shvetashvatara Upanishad 3.8 = Shukla Yajurveda Samhita 31.19
वेदाहमेतं पुरुषं महान्त- मादित्यवर्णं तमसः परस्तात् ।
तमेव विदित्वातिमृत्युमेति नान्यः पन्था विद्यतेऽयनाय ॥
I have realized this Great Being who shines effulgent like the sun beyond all darkness. One passes beyond death only on realizing Him. There is no other way of escape from the circle of births and deaths.
Shvetashvatar Upanishad 4.8 = Rigveda 1.164.39 = Atharvaveda 9.10.18
ऋचो अक्षरे परमे व्योमन् यस्मिन्देवा अधि विश्वे निषेदुः ।
यस्तं न वेद किमृचा करिष्यति य इत्तद्विदुस्त इमे समासते ॥
Of what avail are the Vedas to him who does not know that indestructible, highest Ethereal Being, in whom the gods and the Vedas reside? Only those who know That are satisfied.
Note: I'll update the answer while finding another reference in Upanishads from Veda Samhitas
According to my knowledge, there is only Isha upanishad which is directly from vedas means is the last chapter of yajurveda else all are either from aranyakas or brahmanas.
And about commentaries it depends upon interpretation
brahm-vidya and atma-vidya mainly upanishads explain as far as I know.
Yes philosophy of Upanishads can also be found in Samhitas. According to Upanishads, devatas are actually Brahman. This is described in Shvetashvatara Upanishad 4.2:
तदेवाग्निस्तदादित्यस्तद्वायुस्तदु चन्द्रमाः ।
तद् वेदगुह्योपनिषत्सु गूढं तद् ब्रह्मा वेदते ब्रह्मयोनिम् ।।
That Itself is the Agni, That is the Surya, That is the Vayu, That is the Chndramasa, That is also the starry firmament, That is the Brahma, That is the waters, That is Prajapati.
The same is described in Yajurveda 32.1:
AGNI is That; the Sun is That; Vâyu and Chandramâs are That. The Bright is That; Brahma is That, those Waters, that Prajâpati.
Shvetashvatara Upanishad 4.3:
त्वं स्त्री पुमानसि त्वं कुमार उत वा कुमारी । द्वा सुपर्णा सयुजा सखाया समानं वृक्षं परिषस्वजाते ।
Thou art the woman, Thou art the man, Thou art the youth and the maiden too. Thou art the old man who totters along, leaning on the staff. Thou art born with faces turned in all directions.
Which is identical to Atharva Veda X.8.27:
Thou art a woman, and a man; thou art a damsel and a boy. p. 30
Grown old thou totterest with a staff, new-born thou lookest every way.