YES YES YES its totally rubbish but true. Tried hiring my current helper myself without the help of agency, the immigration gave her a green light, went to Indonesian Embassy to get some forms stamped and the officer said I MUST come via an agency which is approved by them.
The standard agency rate for processing is 3000+ HKD but since I had done the initial paper work the agency took 1500 HKD for getting the form stamped. The agency said they would have to fill in new forms which they did, BUT put in incorrect info. When my helper went again to immigration to get visa on the appointment day they told her of the error and that I had to pay 450 HKD more (150 for each form) because of the overwriting I did to correct the wrong info.
So all together I paid 2500+HKD including visa fee (450 HKD)which is very close to what an agency would charge and save you the headache.