Okay I'm gonna try and articulate at least some of this. What really Gets Me is that while punctuation in English has its own specific set of standards/rules, a lot of how we decide to use it is intuitive, subconscious and highly context-dependent. Look at:
Alaric sat next to me without a word; this time, the silence between us was fraught.
That semicolon usage is technically correct: it links together two related independent clauses into one sentence (just like that colon links up the two clauses of this sentence, and the parenthesis turn this last part into an aside!) Technically speaking, there would be no need to change that sentence. If I was doing a straightforward proofread, I'd probably leave as-is. But! Compare to:
Alaric sat next to me without a word. This time, the silence between us was fraught.
That full stop distills the information into a double-punch delivery. First punch: he sits down. Second punch: the silence is fraught. The quality of that silence, its fraught nature, has been subtly elevated from the surrounding text, which emphasises it far more than when it was attached to the previous clause by a semicolon. If you wanna expand more on that silence, you could stick a semicolon back in:
This time, the silence between us was fraught; if it stretched any further, it was going to snap back on me like a suddenly-released tape measure.
That shifts the focus a little more onto the latter clause. Now it's not just about the fraught silence, but the effect that the silence has on our narrator.
You get something similar with the difference between clauses separated by commas, em or en-dashes and parentheses. As already demonstrated, parentheses are the textual equivalent of a stage whisper (sotto voce, if you will). Dashes are powerful tools for creating both on-page and mental space around a specific idea, thought or action.
It looked at me with its eyes – all six of them – then slid noiselessly back into the black water.
Dashes there emphasise the number of eyes. Maybe that's important because it means the water creature is giving the narrator its full attention suddenly, or maybe you just want to emphasise that this thing has six eyes – point is, those eyes are now the focal point around which the rest of the sentence's meaning coalesces.
You could use commas in that same sentence and be technically correct, but the feel of the sentence would be pretty different. Commas create minimal interruption to the flow of information so they don't create the same amount of information. They're like gently driving over a slight speed bump straight to the next thing, whereas dashes make you stop the car for a moment and look at the view. If that's the effect you want though, then commas are perfect!
Do you see what I mean? Very few of us are actually taught this stuff, and the connotations of different punctuation shifts naturally over time (think of the difference in how older people vs younger people use the ellipsis), but by and large readers will understand what you're doing with your punctuation choices even if you weren't fully aware you were making a choice in the first place. it's like a language all by itself! pretty neat, huh?
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