Those are what's known as knowledge gated games, where your progression as a player is either wholly or mostly tied to your own personal knowledge of how the game world works. Indeed, many of the mechanics may make no sense due to being crude mockeries of how the real world works. But some of them have become so ingrained in the popular consciousness that developers of later Indie Crafty Survival Sandboxy games can rely on the notion that most players will reflexively begin their adventure by punching a tree, and can probably accurately guess what the crafting shape of a pickaxe will be. This is no doubt down to the Earth-shattering popularity of Minecraft itself.

If you ask me, these games refusing to handhold the player and letting them discover things for themselves is part of their appeal. Expecting to be able to dive right in and know everything right from the starting block really rather misses the point. You have to admit that if you've been playing, say, Minecraft since the alpha days, your experience and approach to the game if you spun up a new world right now would be vastly different from your first playthrough, and none of the wonder or sense of discovery would be present.

Gating progression by knowledge (byzantine knowledge though it may be, e.g. in the case of specifically knowing not only how to construct a portal out of obsidian but also activate it by lighting it on fire) mirrors real life in an ineffable way that skill or time/microtransaction/XP accrual gated games can't.

Some games do both. For instance, ask any Dark Souls player. The Souls games are both knowledge gated and very, infamously, exasperatingly skill gated.