Miol

Do not confuse the I129f petition submitted to the USCIS with the DS160 visa application which is submitted to the Consulate in Manila.  You won't be at the Consulate stage for at least a year.

5a would appear to be proper 

No consent needed and they all flew back with me same time.  Its really not an issue, you'll be fine.

K1 and K2 can apply together (separate applications), interview together, have the visas issued together so as to be able to travel together.

As several have indicated, NO consent is needed.

Just let SLEC decide what vaccinations are needed and have them administered during the medical exam.  Peace of mind at no extra cost.

Same situation but wife had daughter with fathers last name. No marriage and no participation on fathers part. Nothing needed extra at embassy or airport. Zero issues. 

General global responses do not apply in this particular case.  Philippine law is unconditional and without the slightest ambiguity that an unmarried mother has absolute sole custody over her child born out of wedlock.  Period.  US Embassy Manila is 100% totally aware of this and abides by Filipino law. As do all Filipino authorities when exiting the country.  She needs nothing whatsoever from the father and everyone knows and accepts that.  It's irrelevant if the father is on the birth certificate or the child has the fathers surname.  The proof of the mothers sole custody is on the child's birth certificate indicating the parents were not married.

I am offering a suggestion to OP about printing out local laws (that differ vastly from US laws), just in case the CO is not familiar.  It is just a suggestion, and OP can take it or leave it.
 
Anyone is free to comment on any page here on VJ.

Nothing required from the biological father.  No consent, no signature, no nothing.  The US embassy in Manila is very familiar with similar family situations.  Don't worry about this.  You don't need to submit any paperwork regarding consent from the father.
 

Yes, you may file another I-129F.  Fill out the section for Multiple Filer Waiver Request under part 3 of the I-129F.  Maybe also provide details about the previous I-129F cases under the Additional Information section on part 8.
 

You will need a waiver.

I think the current VJ record is 5?
 
Maybe time to move to marriage rather than fiancee?
 
https://www.fickeymartinezlaw.com/immigration/k-1-fiance-visa/i-129f-multiple-filer-waiver

No additional permission required.  Please ask Philippines specific questions in the Philippines regional forum so as to prevent uninformed replies.

To the OP:  I would still print out the law to bring to an interview.

She would need to have either court documents specifying sole custody, or printed info of the Philippine de facto sole maternal custody for unmarried mothers.  If you can print out the boilerplate law on this topic, that should suffice.