You are better off to put the name of your child under your surname and do not even dare to include your fiancee's surname in the child's birth certificate to avoid being asked for marriage certificate and this can be used against him on his annulment process. As your child is British passport holder you can easily add his father's surname using DeedPoll when the annulment is final and after you get married.
In reply to my own question for anyone reading with the same or similar question. I received an email today saying baby’s Filipino passport was ready to be collected and if someone else was to collect it, I need to give them authorisation letter, and they need to bring ID and the claim stub/receipt. It took just under 8 weeks in total. My brother should collect it next time he is in London, I’ll let you know if he has any problems.
My brother collected my baby’s passport from ph embassy. No problems there. I had emailed him an authorisation letter and he had id but he said he didn’t need either just the receipt.