Yes it mandatory. Please note that as what you said the company that hired you "assigned" their affiliated Philippine agency for you. This is because the company that directly hired you has to abide by the Philippine law to be duly recognized via the Agency. This is for your own safety, legal and benefit. The reason is that in case something wrong happens to you (God forbid) our government will have to chase this Agency and make it accountable for representing company that hires you, rather than look for them on their own turf. The payment you will give to this agency will be part of your registration to POEA, OWWA membership and Philhealth for 1 year. The above mentioned are legal necessities so that you will not be one of those UNDOCUMENTED OFW's who regualarly by pass this law and when they get in trouble thay want our government to bail them out.

The one thing you need to be careful of is that the company that directly hired you "may" have already given payment to the agency for this process. Just ask that company what the Agency is charging you for this and have they already covered it.