Looking for a game where reading an immersive in-game manual is one of the main gameplay aspects

I haven't gotten to play it myself yet, and it may be more "meta" than you mean by this, but I understand that reading the original game's manual is a big part of the gameplay of The Remake of the End of the Greatest RPG of All Time.

Tunic

- Tunic — You need to figure out the game's manual to know how to play. Souls-style exploration and combat.
- Papers, Please — If you liked Rocket Shop, you'll like this. You are a border guard, checking people's documents and choosing if they can enter. The rules change every day as international tensions grow. Great plot with multiple endings, expressed with just your green and red stamps.
- Hypnospace Outlaw (kind of) — You are a moderator in a fictional version of GeoCities in the last months of 1999. Your training is web pages and crusty point and click CD-ROM slideshows. It's heartfelt story about the impact of technology on society and a loving funeral for that era of the world wide web.

As even further stretches, there is TIS-100 and Shenzhen I/O, both Zachtronics games that have you do programming. The tutorial for TIS-100 just opens a PDF that looks like a crusty scan of an ancient computer manual, like you were learning to program on a C64 or something.

I believe in Deaths Door, we had to gather pages that explained the game mechanics, but by the time you got the pages it was moot point. Tho I might mixing up some games.

Tis-100 is like learning new programming language and do some quiz with it.
If you want similar experience, learn assembly languages, and do some exercise ))

For modern game, try elite dangerous. It doesn't come up with pdf (or I don't find it yet), but you have to do tutorials and watch a lot of YouTube to know how to fly your ship, especially without auto-pilot, auto-docking

Subnautica and Subnautica 2.

The guide is an ingame tablet that's literally your character's survival guide book, recording data on wildlife and tracking your crafting tree.

EXAPUNKS!

It's the dialup 70s, your body is turning into computer parts, and medicine costs 300 dollars a day.

Read the zines, learn to hack. Hack a restaurant. Hack a bank. Hack your body. Hack the planet!

Retro Game Challenge (English version of Game Center CX: Arino no Chōsenjō) and its excellent fan-translated sequel.

Also other games from zachtronics: TIS-100 and Shenzhen IO

I loved Hypnospace Outlaw. Its so nostalgic and yet the surreal aspect of it gives it its own flavor that is separate from the nostalgia.

Not really a manual, but more of a 4th wall derailment into a fever dream of sorts? With a lot of reading while navigating a mystery? And some match 3 tower defence action in between?

Titanium court.


For more of a game with an actual manual focus, try - King of the Bridge.
It’s a game about chess. Mostly.

https://store.steampowered.com/app/370360/TIS100/

The instructions for this game come in the form is PDF written in an in-universe style.

Iron Nest? You drive a turret and you have to read instruction on how to operate it and where to shoot. Not yet come out though.