I know you know Jakarta more than Manila but, what you said doesn't really do justice to the many, wonderfully-looking malls available all over Metro Manila, especially in the Central Business Districts (Makati, BGC, Ortigas).
With the exception of a few older ones, all malls by Ayala, SM, Robinson's, and Megaworld, are shiny new, perfectly air-conditioned, and packed with shops from the more conventional fast foods to exotic and fine dining restaurants, and pretty much any commercial establishment you could think of, from electronics to sports equipment, spas to dental clinics, and even several essential government offices.
Metro Manila can be hell, with all the pollution and the traffic on its main artery (EDSA), so malls have been designed as proper oases for people to stroll, dine, and shop. Believe me, it's as sanitized and refreshing as it gets, over here

In terms of hygiene, in my 7 years here I have never had a single problem with a mall restaurant, from a humble Jollibee to a posh steak house. Mall restaurants in Davao tended to be a little bit more run down, compared to Manila, but never to the point where I would see a roach or similar insect roaming free and would be worried about the quality of my meal. Never had a single episode of food poisoning, either. Independent, smaller restaurants tend to have much less strict hygiene standards but, to be honest, I am rarely attracted to those, especially if a mall is nearby and I can count on a more established brand.
As for gluten-free and vegan options, as we know Filipinos are some of the world's best gluttons and omnivores. I am not a vegan but agree with you, one would be hard-pressed to find establishments catering to "niche" diets. Restaurants offering healthy meals like salads with organic veggies, unsugared smoothies, and the likes, are quite abundant, though they tend to exist only in the posher malls.
Just to give you an idea, this is a mall that's less than 10 minutes walking distance from our home. It's called Podium, owned by SM. It has been substantially renovated a few years ago and it looks like something even Singapore would find hard to beat.

