To quote TLDC's own stuff: "https://www.tagaloglessons.com/lessons/stress-accent-marks.php"
As far as I know the admins here are pretty consistent in using them in educational materials and using them correctly. Perhaps you've mistaken a change in accents to mean incorrect usage, but stress and glottals change and disappear based on other things that happen to the root word.
A quick look at the Komisyon sa Wikang Filipino's FB page shows that even *they* aren't using the diacritics. The reality is that natives can, and do, use imperfect orthographies. Just look at English.
As a person who has lived in the Philippines since about 2017, I can say that I almost never see (nor do I expect) the diacritics. AFAIK the govt stopped using them in publications some time in the 1980s as well.
Once you learn what exactly the diacritics represent, you should be able to write them without having seen the word. If you're wanting to spell baba with the down stroke to mean chin, or baba with the circumflex to mean bottom, you'll know that the latter has a glottal x[baba?] so it gets the circumflex.
BAba, baBA? (xsampa for my convenience)