The Pali commentary fills in some of the gaps. Here is the relevant footnote from Ven. Bodhi’s translation:
While Rāhula was following the Buddha, he noted with admiration the physical perfection of the Master and reflected that he himself was of similar appearance, thinking: “I too am handsome like my father the Blessed One. The Buddha’s form is beautiful and so too is mine.” The Buddha read Rāhula’s thought and decided to admonish him at once, before such vain thoughts led him into greater difficulties. Hence the Buddha framed his advice in terms of contemplating the body as neither a self nor the possession of a self.
In the MN62 the Buddha first tells Rāhula to contemplate the body (rūpa), and only when asked by Rāhula does he add the other four khandhas.
When Rāhula has been been admonsied, he sits down at the foot of a tree to meditate. Ven. Sāriputta comes along, sees Rāhula and thinks he is meditating, and he encourages him to develop mindfulness of breathing. The commentary adds:
Ven. Sāriputta, Rāhula’s teacher, gave Rāhula this advice unaware that he had already been given different meditation instructions by the Buddha. He was misled by Rāhula’s cross-legged posture into thinking that he was practising mindfulness of breathing.
Later Ven. Rāhula approaches the Buddha and asks him how to develop mindfulness of breathing. The Buddha then teaches him meditation on the elements, the divine abidings, asubha meditation, and meditation on impermaence, before explaining mindfulness of breathing. The commentary explains this as follows:
The Buddha here explains the meditation on the four great elements rather than mindfulness of breathing in order to dispel Rāhula’s attachment to the body, which had not yet been removed by the brief instruction on the egolessness of material form.
Whether the commentary’s explanations have anything to do with what actually happened is hard to say. It could just be an ex post facto justification.
Ven. Analayo has studied this sutta here, see p.97.