As others have stated......your fiancee can secure his UK CNI from UK and it can be exchanged for local (Philippine) CNI at the Embassy by you. He does not need to be present.
However, under Philippine law there must be 10 days between application of the marriage licence and the issue of the licence. Legally you must both be present.
Without appearing to 'flog a dead horse' this is made "Just for the record."
The CNI is a Certificate of no impediment (sometimes called Legal Capacity to Marry)
This certificate provides evidence to officially authorised people that the marriage will be recognised as a valid marriage in both Philippines and the country of the foreign spouse.
A valid CNI is required by Philippine law.
The Foreign and Commonwealth Office states:-
From Article 21 of The Family Code of The Philippines:-You should check with the authorities in the country where you are marrying whether they can accept the CNI as issued by the UK registrar or if it must be exchanged for a locally acceptable version (ie. a certificate in the local language) issued by the British Embassy or Consulate
In connection with the Marriage Licence the Executive Order No.209 (The Family Code of the Philippines)When either or both of the contracting parties are citizens of a foreign country, it shall be necessary for them before a marriage license can be obtained, to submit a certificate of legal capacity to contract marriage, issued by their respective diplomatic or consular officials.
States:-
Just for completeness it goes on to state:-Art. 17. The local civil registrar shall prepare a notice which shall contain the full names and residences of the applicants for a marriage license and other data given in the applications. The notice shall be posted for ten consecutive days on a bulletin board outside the office of
the local civil registrar located in a conspicuous place within the building and accessible to the general public.
This notice shall request all persons having knowledge of any impediment to the marriage to advise the local civil registrar thereof.
The marriage license shall be issued after the completion of the period of publication.
The highlighting was done by me and does not appear that way in the Family Code.Art. 20. The license shall be valid in any part of the Philippines for a period of one hundred twenty days from the date of issue, and shall
be deemed automatically canceled at the expiration of the said period if the contracting parties have not made use of it.
The expiry date shall be stamped in bold characters on the face of every license issued.
There are always 'under-the-table' ways to circumvent the rules.....but often these can lead to difficulties further down the path.
Hong Kong marriages are pretty trouble free.....suggest you do some research as it might help if you both find time pressures too difficult to manage.
To get married in the Philippines will take minimum 14 days. Having said that, not so many folks have actually achieved but it has been done. Not recommended.
Without good planning, you may not actually get your marriage licence within 10 days.
Maybe that 10th day lands upon a holiday or a weekend when the office is closed.