Most of the guides and rotations I've read are in fact developed using parsing and simulation to figure out what's actually optimum, down to exactly what gear and materia is actually best in slot. They didn't magic the information out of nowhere, but odds are good that a fair number of people didn't do it solely with what's available in game either. I'd imagine the people who made the mods and did the math put in the time to learn how the game works, but I also don't know anything about how they were actually put together so I dunno really. And I mean, I'm sure it's entirely possible to figure out something fairly close to the most optimal rotation just from the game alone, but how many people are going to actually do that? Easier to look up a guide made by someone who did the work already, and even better if they've got quantifiable data and tools to help define what the best options actually, definitely are.
I don't run a parser and never have but one example that ZedxKayn's post reminded me of is this bard I used to play with back in Heavensward who was absolutely convinced that they were doing more damage without using minuet EVER than a bard who is using it. Based on the numbers that could be found online though... they were consistently doing less than half of my damage, and I was by no means an amazing bard. They thought they had the class figured out based on what the game was telling them but they very clearly did not. Bit of an extreme example since it involves someone actively ignoring part of their kit, but I've seen enough people who were very confidently wrong that it wouldn't surprise me if there were plenty who genuinely believe they've figured it out from just playing the game when they're really way farther off base than they think.