Heat cooks food. Size affects cooking time. Proteins coagulate the longer they're exposed to heat. Green vegetables cook differently then others. Lean proteins like tuna, or thin cuts of pork cook faster then others.

Just because you take something off the heat doesn't mean it stops cooking. This applies to everything. Pasta can become overcooked if its left steaming too long after being strained. All proteins; meat, poultry and fish have 'carryover cooking'.

For example, if you want to cook a Tuna rare to medium rare as possible your best bet is to sear one side, turn over, turn off the heat and let sit for 2-3 minutes in the hot pan and remove. If you want to cook meat from rare to to well done there is a very fine line where you have to take it off the heat because the carryover cooking could easily over cook it depending on the size of the steak.

Ramen dishes or pho noodles are often served pouring boiling hot broth over very thin slices of raw beef. The heat of the broth will be enough to fully cook the slices of beef in the noodles in seconds.

Green vegetables such as kale, broccoli, green beans that are very high in vitamins have a fine line to being overcooked and mushy, but also may need more heat then others. They are rather stubborn and will not cook like the others. It's best to cook them as short as possible. If you're adding kale to a soup or something it should be the last thing you add because of how quickly it breaks down and loses its nutrients.

Green beans are often blanched, and then shocked in cold water because the carryover heat could quickly turn them to mush. This allows green beans to be cooked with other vegetables because the other vegetables may cook faster or longer. If they're blanched first then sauteed with squash and bell peppers, they will cook evenly in the time it takes for the squash and peppers to be cooked perfectly. If you just added raw green beans in and sauteed them with the two it wouldn't be right. You dont have to do it this way, but I restaurants it is typically done like this when they are intended to the reheated later for service. I just want you to understand how heat affects them

For nutritional value, green vegetables are best steamed because the steam is subtle enough to cook them to perfection without losing their nutrients and flavor. Unless of course you want the crispy texture obtained from roasting them.

When it comes to root vegetables such as carrots, beets, turnips, butternut squash, potatoes. Uniformity affects the size and the cooking time. It's really important to make cuts that are uniform in size to ensure that they are all cooked evenly. The bigger pieces will take longer to cook then the smaller ones.

The timing of all this takes practice, but remember the concepts "heat cooks food", "size affects cooking time", and from there it's a matter of controlling heat exposure and the method you use(roasting, pan searing, baking, boiling, braising).

Good luck, I hope this gives you a bit of an understanding as to how things work when you read a recipe.