Your English teacher was wrong, for starters. The presumption that all writers develop their work the same way is flat-out incorrect. I know writers who can only write with outlines, writers who don’t use outlines at all, writers who believe they’re writing out events that happened in some other place in the multiverse, and writers who strongly attest to just the opposite. 

Depending on who you ask, writing is intellectual or personal or philosophical or spiritual or any combination of the above, and no two people approach it identically. Writing, like all art, is as personal an alchemy as the construction of your own identity. 

So it’s entirely possible Hussie is a writer who could indeed have thought a lot of this out ahead of time. I don’t know the guy and am not in the habit of speculating as to his nature or allowing ideas about what’s “possible” for a writer to influence how I read the text, because usually what people think is “possible” is just a bunch of self-limiting bullshit.

That said, I don’t really know how Hussie wrote the story, beyond a few methods that are beginning to seem self-evident to me. We’re lucky in that one such method is one he’s discussed himself, presented here through @curlicuecal ‘s excellent roundup of Hussie’s quotes on writing:

The takeaway here is that Hussie is a very rules-focused author, who values consistency and strict adherence to the parameters he lays out.
This is specifically about character writing, but Homestuck is a rules-focused narrative in all things, so it’s easy to extrapolate elsewhere:

The Alpha Timeline, Classpects, Roleplay, The Active/Passive Spectrum, Denizen symbolism, Dreamselves–all have corresponding sets of rules, whether they be guides for behaviors, logical consequences to actions taken, or the fundamental structures of the setting itself.

It’s also demonstrably true that Hussie is something of a culture remixer, who will freely adapt entire plotlines from other sources for a particular character’s arc if it’s useful to his goal.  

So I’d suggest that this hypothesis is somewhat likely:
At least insofar as the Gnostic symbolism that pervades the entire story goes, you’re mixing up cause and effect. 

Hussie didn’t need a second draft to “add” symbols to his story, because Homestuck is built around the symbols in the first place.
It’s worth noting that Homestuck itself puts a massive emphasis on the power of Symbols through the TRAGICALLY overlooked Drunk Rose District section:

So, for example, Hussie didn’t need to know every minute twist and turn of Caliborn’s ridiculous story in order to build him up as a compelling villain–he just needed to start Homestuck’s story with the understanding that it was about being “Trapped” in a flawed world created by a “Yaldabaoth” figure:
a flawed, evil Creator God associated with the Sun. 

This means Hussie could use the symbol of the Sun to stand in as a symbol for Yaldabaoth/the central antagonist, which is precisely what we see him do:

And the details of the antagonist’s nature could be developed and presented later, linking the character to the Symbol explicitly in any number of ways:

Like the red sun being presented later in Caliborn’s artwork, “Homosuck”–represented by his red cheek spiral, no less.

Hussie could also hypothetically build from the symbolism already associated with Yaldabaoth to flesh out the character further. All it would take is some cursory research on, say, Wikipedia or other freely accessible texts like Jung’s 7 Sermons. 

The Demiurge is sometimes described as an Angel, and through association with Samael, specifically an Angel of Death. There we get LE embodying Death to Troll-kind, and Caliborn and Calliope’s Cherubic origins. So on and so forth.

This is the logic that guides my approach in researching everything Homestuck presents, not just Caliborn. The Classpects, the Denizens, particular character beats–everything. So far, I think it’s been pretty fruitful, so I might be onto something with all this.

And doing this kind of freeballing, primarily online research for mythbuilding would also make a lot of sense if Hussie were, for example, writing primarily for an online audience known for researching and analyzing pretty much everything the story presents.

It would in fact be quite efficient to include some references to Wikipedia and then litter the story with thematic and symbolic callouts, letting the fandom pick up the threads and apply them to the plot, which itself would benefit from being able to focus on itself without having to take the time to explain and break down every symbol and reference.

Again it’s worth saying that this is just me guessing based off what I’ve seen in Homestuck itself. I have no idea if Hussie actually approached the story at all like this. I could well be wrong.

But whether or not it’s true in Hussie’s specific case, it’s certainly a way one could plausibly construct a story like Homestuck, if one were inclined to write a very complex story with profound symbology and approached writing as a process of setting and then holding to a series of rules.

So whether or not it’s true here, I think it lends a certain logic to how stories like Homestuck could be written, and that makes it a valuable exercise in critical analysis and in considering how I might like to write things someday, myself. 

Writing works like this is certainly not impossible. 
It just takes a little foresight, persistence and commitment to a certain work style, and good foundational design.