Two explanations fit, and they do not contradict each other.
1. The Constitution introduces the offices before it introduces the body they sit in. Chapter I creates the President, the Vice President and the Council of Ministers. But the Parliament described in Chapter II includes the President — “the Parliament of India… composed of the President, the Lok Sabha and the Rajya Sabha”. You cannot describe Parliament until you have first created the President. So the order is logical rather than a ranking: define the office, then define the assembly that office is part of.
2. It reflects how the two organs actually work together. The Executive is not outside Parliament in our system — the Council of Ministers is drawn from the MPs of both Houses, most bills are introduced by the Executive, and it is the President who summons Parliament and gives assent to its bills. Placing the Executive first shows how tightly the two are woven together, which is the distinguishing feature of a parliamentary system as against a presidential one.