There are at least two ways of approaching TOS- what was onscreen, and what was intended. I tried to point this out earlier. What is onscreen is an objective fact. What was intended is a much more nebulous thing requiring us to answer basic questions like "intended by whom
?" and "intended in what sense?" This last question is particularly difficult to deal with and has created a stumbling block here:
Was it really intended that one side of Enterprise lacked details and had electrical wires protruding?
What was intended with the bridge turbolift- on-axis with the main viewscreen internally or off-axis with the bow externally? Or neither? Or both?
Was it really intended that the transporter could take matter, convert it to energy, transmit the energy to a location and convert it back to the original matter? Or was the intent just to get the story going as quickly as possible? Or was it something else?
In other words, there are questions where the intent is rather obvious because some effort was made to hide (or feature) what was going on. But there are many, many questions where intent is not at all obvious. In some, the contradictions were insolvable and thus ignored. In some, they were deemed irrelevant and thus ignored. And in some, the time, money and/or talent just wasn't there to deal with it.
When dealing with the conflict between Franz Joseph and what was onscreen, you are definitely dealing with this last question. There was an imagined Starfleet, and there was the Starfleet that could be portrayed. There was an imagined 23rd century, and there was the 23rd century that could be portrayed. These things were sometimes harmonious, like a glimpsed view of a part of something much bigger. But sometimes what was shown onscreen was in clear contradiction of what was intended by one or more of the people responsible for putting the show on your TV screen.
Franz Joseph tells us he was trying to show us what was intended but for one reason or the other in some cases wasn't shown. Whether Gene Roddenberry was using him and his work to keep Star Trek alive or really agreed he showed what was intended, we don't know. 1973 Roddenberry tells us one thing. 1980s Roddenberry tells us another.
I think that looking at the question of Franz Joseph versus canon is best examined in this way: In fact, there is no conflict at all because they are entirely different things. One does not and cannot purport to be the other. Canon cannot be interpreted as the totality of what was intended nor was it ever intended as such. And Franz Joseph, at best, offered an imperfect and incomplete version of what was intended.
So, I think an ideal solution would be to attack these problems seperately. Document canon
with attention to the finest detail. AND interview, research, collate and collect every scrap of evidence to ascertain the intent
. And acknowledge that these are different and largely seperate things and that however much you do, you will never be able to fully uncover this nebulous, evolving, thing with multiple meanings called intent, but that by trying, you reveal an entirely new but related Star Trek that makes it alive in our imaginations.