For example, if you pick up a bit of blue clay, there might be some flavor text in the tool tip. It might read something like: "People used to make useful pottery from clay. The pieces this particular type of clay produces can't handle heat sources more extreme than a simple cook fire." This implies 1. The player can do something useful with this item. 2. There is at least one other type of clay with unique properties the player should look for. 3. There is a reason to expose clay to extreme heat, just not this kind. Once the player has formed an item from the clay (the pop-up should take care of this), the unfired piece might read: "An unfired *insert item* made from clay. These were once fired in great kilns, but the less fortunate found that a small hole in the ground suited their purposes for their simple pottery." This tells the player 1. This needs to be fired. 2. A proper kiln is not needed to fire it (if they are knowledgeable on how pottery is made). 3. They should try putting it in the ground (at which point the pop-up informs them on what needs to be added), and use a heat source (like fire) to harden it. It gives the player the same information, and gives them a cookie-crumb trail to follow, but gives the process a more natural flow. Rather than sitting down and reading a Wikipedia article on it overnight, they get to think about what is being told to them (presumably by their character's limited knowledge), and try to act on it and experiment a bit. If they really want or need the help, particularly with the smaller details, the handbook would be there. I just really don't enjoy it when a game is telling me to do this and do that, and this is exactly how it's done and leaves no room for me to just stop and *think* about what I'm doing. Since the game is giving me few to no hints outside of the handbook, it just feels like an extended, handhold-y tutorial to me. It might not be giving me pop-ups every few minutes, but it still feels that way. Obviously, having the game clue you into every niche mechanic like this would likely be unfeasible, but having a line of progression through the more basic, important stuff would go a long way, I think.
Some more examples might be like:
Fat: Edible in a pinch, but often used as a sealant against the elements. Hunters found it convenient that it was packaged in with their kills, particularly in the autumn when preserving food and hides was especially important.
Native metal chunks: A surprisingly pure piece of *insert ore type*. It likely hasn't moved far from the source.
If any of that makes sense?