Basically. Yes, lists and pauses account for part of it. Appositives are basically non-essential parts of a sentence and are separated from the rest of the sentence via commas as well. For example:
The Great Gram Grape Jam Company, created by Richard Gram himself, was famous for making jam which came in eco-friendly containers.
In that sentence, the 'created by Richard Gram himself' part was not necessary for the sentence to make sense grammar-wise. The sentence would have been fine as the following:
The Great Gram Grape Jam Company was famous for making jam which came in eco-friendly containers.
For these non-essential parts of the sentence, we use commas.
Now, lets see if you can correct the comma mistakes in this post of yours. If not, that's fine, we'll work on it.
Lightning met flame, as the source of Hikaru's magic signature sizzled and faded out. A sphere of regular fire. She wasn't so stupid as to leave her magic signature, unsuppressed. And this mistake, would be the beginning of Mokai's downfall.