1. This will vary from setting to setting and person to person. There isn't one true way of "learning" spells. Each wizard will do it differently, each druid, etc. The patterns for any given spell have the same key points, but how you get those into you will vary.
2. That's the whole point. When you shoot a lightning bolt, you're not creating a set of alternate charges. It doesn't and can't work that way. You're imposing an area of a particular "lightning aspect" on the reality there, with appropriate results. And in a world like this, that has fixed effects. Why? That's not known (or possibly even knowable). My home setting has those effects as being chosen by the current God of Magic, who was "promoted" to that position after he broke the world and inadvertently caused the deaths-by-self-sacrifice of all the previous gods. Literally, those effects are fiat. Now in-universe, it's not that spells have these nice crisp edges. But for game purposes, the effects must be clear-cut. Going any further results in madness (because it's an endless rabbit-hole) or fights over who remembers their physics the best (or can convince everyone else that they do). It's also drastically unbalancing for the game, at least in a D&D context. It lets magic-users (and only magic-users) be creative with their effects, letting them do even more of everything than they could before. And that's not fun for anyone except the power-mongers.
A fireball doesn't heat the air by exothermic reactions. It imposes a fire aspect over the entire area. So hiding underwater doesn't work because the water gets the same fire aspect as the air did. Not all ice aspects are freezing aspects--only things that are "tagged" as such have those aspects. And there isn't (by choice) a binding theory that connects and lets you alter these effects. All the casters know is that if you do this pattern, you get a fireball, with such and such parameters. Alter even one little bit, and you get a fizzle except as trained by esoteric studies, such as by arcane schools of thought. Sorcerers (by virtue of their bloodlines) can tweak things more than most, but still only a limited amount.
Edit: You're fundamentally asking for a grand unified theory of magic. And that's just not feasible or playable. None of the worlds can be rich enough to accommodate that, and it requires basically warping the entire ruleset around a single setting. Which is something I fundamentally oppose. Single-setting rules are, to me, a total waste of space, because I want to world-build and world-break. And I can't do any of that when I'm stuck in someone else's world. I want rules that get out of my way and let me tweak a lot of the underlying "physical laws" while still maintaining consistency and ability to use them. This necessitates a lack of expressed theory. Because otherwise you're nailing down all the interesting things for me to mess with, and making breakage that much more likely.