Upvote:3
As usual, it depends. I haven't been to all Philippines (only to 14 or so cities), so take this with a grain of salt.
Every public toilet I used there was reasonably clean. Most weren't exactly as shown on your link, and some (for example on a local market in Cebu) didn't have running water (there's a bucket of water nearby and you flush with a ladle), but it didn't look or felt filthy. From my experience it's similar to Thailand, and way above a typical toilet in India.
What was common, however, was the lack of toilet paper. Even paid toilets sometime (not always) had only tissues, and usually for extra fee - although minor.
And as you guess, pay toilets and those closer to touristy areas are generally cleaner and more stocked.