Short answer. They are governed separately. Labor Code Article 49 expressly states that this article shall not include apprentices, learners, and handicapped workers, since those are governed by other appropriate provisions of the Code. The Council's general manpower training administration under this article is not the framework that applies to them.
What the law says
This Article shall not include apprentices, learners and handicapped workers as governed by appropriate provisions of this Code.
Labor Code, Article 49 — Administration Of Training Programs. Read the full provision →
What the Council administers under this article
Article 49 gives the Council, acting through the Secretariat, a broad administrative role over manpower training generally. It shall provide, through the Secretariat, instructor training, entrepreneurship development, training in vocations, trades and other fields of employment, and assist any employer or organization in training schemes designed to attain its objectives under rules the Council establishes. The article also puts the Council in charge of coordinating and reporting requirements, so that manpower training schemes across the government and private sector line up with national development programs and skills standards.
The express carve-out for your apprentices and learners
The article closes with a direct exclusion that answers your question: this Article shall not include apprentices, learners and handicapped workers as governed by appropriate provisions of this Code. That means the broad coordinating and reporting scheme Article 49 sets up for manpower training generally does not reach your company's apprentices or learners. They are carved out by name, not left inside this article's general coverage by omission.
Why they sit under separate provisions instead
The reason for the carve-out is that apprentices, learners, and handicapped workers already have their own dedicated rules elsewhere in the Labor Code, tailored to how those specific arrangements work, rather than being folded into the Council's general manpower-training administration. So if you are trying to work out what rules govern your company's apprenticeship or learnership programs, the answer is not found by tracing them through Article 49's coordination and reporting scheme; it lies in the Code's own provisions specifically addressed to apprentices and learners as such.
What the coordination requirement covers instead
The coordination duty this article does impose reaches other kinds of manpower training: existing manpower training programs in the government and in the private sector shall be reported to the Council which may regulate such programs to make them conform with national development programs, particularly where skills standards are involved. That reporting and potential regulation is aimed at general vocational and trade training programs, not at apprenticeship or learnership arrangements, which the article's closing sentence removes from its reach entirely and leaves to the Code's dedicated provisions instead.