Before you read on. These are things that I fond one way or another, that was kind of rewarding to figure out either by accident, someone else or by reading the emails. So read at your own pace. I'll try to start with what I think it's more common knowledge and go towards what I think people might actually not know.

1. NIGHTMARE REPLAY you can replay nightmares if you look at the figurines in your room.
2. WEATHER FORECAST once the weather station is available you can check the map, and press R3 twice, and you will see where there is rain. And by pressing up or down can see if the rain will move, stop or continue in the next 10, 20, 30 minutes which you can either fast wait in a rain shelter, or you can wait it out in real-life minutes.
3. HOVERING CARGO You probably already know you can link carts together like a train, and link them to you, but you can also use the hovering cargo as a hoverboard to ride downhill, pressing L2/R2 to stop and square to push forward, but even more fun is you can link a cargo behind you while you are riding the hovering cargo.
4. CHYRALIUM CRYSTALS Killing BT's will yield crystals you can pick up where they die.
5. SECRET RIDE MOTORCYCLE There is a special *faster vehicle item you can find in the waterfall close to mama.
6. REQUESTING HELP WHEN FIGHTING BTS If fighting a large BT you can call for help by pressing the PS touchpad button to have another "player" help you with equipment.
7. OTTER HAT The "Otter" hat which is given by the cosplayer (which is actually Conan O' Brian) actually has a use. It makes you swim more swiftly.
8. TRADING WITH PORTERS If you see other porters, they will sometimes give you stuff, and you can also equip something in hand drop it for them and sometimes they will pick it up, this also gives you an achievement.
9. SECRET PREPPERS There are two secret preppers in the first area, which I personally missed twice. If you look at the map and press "R3" to check the chiral network, blank spaces will ALWAYS have a prepper or outpost somewhere within that region.
10. ADVANCED WEAPON FIGHTING using lethal rounds on BT cause some damage, using hematologic rounds also causes some damage. However, if you expose a wound with a hematogenic bullet and then shoot with lethal rounds BT will take increased damage. It is also possible to throw a hematogenic grenade to a BT and shoot through the mist with lethal bullets effectively coating them with hematogenic properties and cause extra damage.
11. USING 1ST PERSON TO ADVANCE FASTER You can hold L1 and thread through some difficult terrain like snow a little bit faster. Whether this is a bug or the fact that looking closer at your feet stabilizes your walk is a fact only Hideo Kojima's team would know.
12. LOST CARGO MECHANICS If cargo is passed on from player to player, it's priority increases, you also get likes for entrusting cargo to other players. So feel free to grab all the cargo in a locker you see and entrust it to other players as you will get likes and raise the value for the next player that does complete the delivery!
13. EYES UP HERE LADY! If you look at sam crotch long enough he'll punch you.
14. DAYDREAMING if you check up on BB long enough you'll see some special cutscenes.

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That is all that I know for now. If you have any other tips please share. If you found any of these useful please upvote so other people can see. Also, please keep clean of story spoilers. And anything you're not sure if it's giving away too much, just hint at it. I haven't finished the game yet.

I also made a list of simple of basic equipment tips

*EDIT: I'm updating both these lists as I go and actually found more interesting things that ought to be mentioned to either understand mechanics better or avoid missing possible secrets. Also, thanks for all the feedback.