If it doesn't flow back to his design to whom or what does it originate with?
You misunderstand me - let me expand on what I mean.
Chon-Ji is indeed General Choi's invention (or one of his lieutenant's anyway). But the moment the form is learned and taught by someone else with considerable knowledge and experience himself, part of him inevitably bleeds into the instruction and becomes part of the transmission itself. This is inavoidably so, particularly if the method of instruction in the first place was something like a book or manual and the reader WILL fill any gaps with his own pre-existing knowledge, intentionally so or not.
Who do you think wrote the field manual? The lineage explains how Chung Do Kwan habits influenced an instructor's performance and progeny.
My educated guess, not having a copy myself, is that General Choi was the attributed author. As for Chung Do Kwan habits, sure. You are what you are. If you practice a certain method and then later convert to another set of forms, it's likely that your new forms will show evidence of your prior training. This actually solidifies what I said above about people coming into the Chang Hon patterns with different assumptions because they stem from different lineages.
How do you develop the knowledge to determine if you like what your instructor says or if he was correct? Jim Jones had his minions drink Cool aid. Throughout history students have done that, learning that the earth was flat, and the sun revolved around the earth.
Most people obviously won't advance to the level of mastery enough that they KNOW what is correct or not for themselves, much less for 'most' other people. But a small number will. To link it back to a more concrete example, rather than talking about Jim Jones, I'll point out that I think how Jhoon Rhee taught the Chang Hon patterns is perfectly acceptable though it deviates from what is written in the Encyclopedia. I'll go ahead and say the same for little groups here and there, ATA off-shoots or not, that also use the Chang Hon patterns. It's fine enough if they know the weapon, the target, and intended outcome for each section of *THEIR* forms as that level of understanding is broadly accepted as necessary for BB level.
Would you tell Mozart that the right way to perform his song was how some instructor told you to perform it as opposed to how he wanted it performed and designed it to be performed?
People make remixes all the time, Mr. Weiss. Or they add their own spin on things. See the Star Spangled Banner for example. Andrew Lloyd Webber became a very successful modern composer just by changing around some of the classics and then working with a team of lyricists for his productions.
I'll go back to older martial arts than TKD as well. Sets are modified and adjusted all the time there.