An ordinary complaint runs under ss.29 and 30 of the Estate Agents Ordinance and is about a licensee's conduct. If it is substantiated, the powers available are admonishment, reprimand, conditions on the licence, suspension of up to 2 years, revocation, a fine of up to HK$300,000, and orders about the costs of the proceedings. A fine is not compensation, and it does not go to the complainant. In the Authority's own words, a claim for damages caused by misconduct or breach of duty is not within its jurisdiction and you should pursue it through legal proceedings or alternative dispute resolution yourself.
The s.49 route is a different scheme, in a different Part of the same Ordinance ("Disputes as regards Commission, etc."). It decides the money — the amount of the commission, how it is calculated, or how it is payable — and only where both sides agree. Under the Estate Agents (Determination of Commission Disputes) Regulation (Cap. 511D), s.4(1), it is started by a letter signed by both parties stating that they agree to refer the dispute under s.49, plus a HK$500 filing fee from each party; s.4(2) says the proceedings are deemed to have commenced on the date the letter and the fees are received.