Āpastamba 1.1.28-29: If the proper time for initiation has passed, he shall observe, for the space of two months, the duties of a Student, as observed by those who are studying the three Vedas; after that he may be initiated; and after that he may be instructed.
Manu 3.1 (Period of Studentship): Duties relating to the Three Vedas should be observed under the Preceptor for thirty-six years, or for half that period, or for a quarter, or precisely till they have been got up.—(3.1)
Vālmīki Rāmāyaṇa 6-105-13: He [Surya, the sun-god] is the lord of the sky, the disperser of darkness, the master of the three Vedas (viz. Rik, Sama and Yajur), the sender of thick rain, the friend of water and the on who courses swiftly in the path of the sky.
Chāndogya Upaniṣad 2.21.1: The three vidyās [the Ṛk, the Yajuḥ, and the Sāma] are together the hiṃkāra; these three worlds [the earth, the space between the earth and heaven, and heaven] are together the prastāva; fire, air, and the sun are together the udgītha; the stars, the birds, and the rays are together the pratihāra; serpents, gandharvas, and the ancestors are together the nidhana. This Sāma resides in everything.
Trayī vidyā hiṃkāraḥ, the three Vedas [the Ṛk, the Yajuḥ, and the Sāma] are the hiṃkāra; ...
Is the reference usually to the three types of Vedic mantras that can be present in any of the four Vedas or to the three Vedas, namely, Ṛgveda, Yajurveda and Sāmaveda? If it's the latter, why is Atharva Veda excluded from the list?