The Darkest Danger and Horror Dolls achievements are story/progression related and therefore should be unmissable. It is really weird you didn´t unlock them on your first play. Maybe on the second play they will be unlocked. They are not too far away in a story so it is worth a try.

The God Almighty achievement unlocks after collecting 100 secrets. No need to find them all.

That's what I figured. I even went back to both areas to try and trigger them but nothing. I guess I'll try and play it again at some point but for now I feel a little burnt out.

The Darkest one is best achieved while encountering "him" in the Flashpoint caves for the first time. Try to look around and wait to "him" to appear while avoiding any encounter with "him".
The Horror Dolls achievement should be self-explanatory, e.i. find/meet those damn dolls. It should work by any means...

引用自 Lindylou：

I guess I'll try and play it again at some point but for now I feel a little burnt out.

I have finished this game many, many times and never felt burnt out. On contrary - no rest until it´s over! Give it a try. The achievements should be working. See here;
https://psteamcommunity.yuanyoumao.com/app/313630/discussions/0/2962769352286338111/

Gonna play some portal 2 again and come back after to try and get them. Just need to cleanse my palate. I mean I definitely encountered the spiky cloud and those creepy dolls, both scared me ****less. Maybe I died too many times before finally figuring out the cloud. Actually just thinking, my internet connection was poor a couple weeks ago, maybe being offline messed with it. Thanks for your help, I'll update if a second runthru grabs the achievements.

So, how did it go? Did you try that second run-through? I am not able to see it on your profile.

I've been preoccupied with other games this year but saw your reply so thought I'd skim through to those parts and check it out and this time they did register! Got them :) Must've been my poor connection.

I´m glad you did get them.

Me too, it was annoying having those missed.