Why the sequence is what it is. Every step has a reason, and knowing it lets you improvise.
Parboiling: Raw bones release blood and protein as grey scum at the first boil. You deliberately boil that out separately and throw it away, so the real broth starts clean. You can only match this with very long skimming. Many Vietnamese cooks parboil 5 to 10 minutes, some longer; 10 to 15 minutes here is the safe route.
Charring: Onion and ginger need contact with strong heat until the cut sides are dark, in places black. The sugars caramelize and give the slightly smoky sweetness that separates pho from a plain beef soup. Some of the charred skin gets rinsed off later, not all of the flavor. You toast the spices briefly because the essential oils open up with heat, but turn bitter with too much.
Simmer, do not boil: The surface should only shiver, with the occasional small bubble, roughly 90 to 95 C. A rolling boil whips fat and protein flakes into the liquid, and they never settle again. Keep the lid half open so not too much water evaporates but the pot does not boil over either. If the level drops a lot, top up with hot water, not cold.
Seasoning at the end: Because water evaporates and the broth concentrates, early seasoning is guesswork. Salt and sugar go in at the end, fish sauce in stages. One spoon of fish sauce often makes the difference between good and right; it should not taste of fish, but of depth.
Defatting: If you have time, chill the broth overnight. The fat collects as a solid layer on top and lifts off in one piece. You get back exactly the amount you want in the bowl, and the broth is clearer.