I do agree that it gets complicated towards the end and if the baby is born in the Philippines. According to the airline, one would need a medical certificate only if more than 35 weeks.
The medical certificate is to ensure that she won't go into labour during the flight.
My wife is currently ~20 weeks pregnant and her visa application is into its 10th week. I seriously don't think that it will take another 15 weeks for the embassy to reply. I've sent a formal letter to the embassy about my wife's pregnancy last week, which hopefully would not delay the application too much.
Also, its nice for her to spend time with her experienced parents as the first few months was very hard for her being sick. She is much better now after the first 3 months.
Ideally, it would be nice to plan everything in life, but sometimes you just can't.![]()