The premise behind those concerns is a pretty narrow imagination of what a generation ship is or might be.
It is a generation ship. As the name states, the dictator will die, any initial specialist will die during the journey.
It is not a submarine, they all will die, multiple times, generations.
You have to teach new personnel. Is that possible without a replica of structure which made it possible? Not sure about that. Teachers are not equally good, there are better teachers and not so good teachers.
Personnel might be better for a job or not so good at the job.
If you do not have an excess of people to choose from, this situation begins to degrade, as you have to use what you have and can not be picky about choosing peoples for a position. In that situation, the whole expedition is under the probability to fail.
In that limited situation, where each one should do what he is being told to do, you have not only have to abandon those freedoms you are concerned about, but all others too. And you have to do so, not only on that ship, but before that ship starts. You have to test whether your system works, for a few generation possibly without the ship flying. Probably even before the ship is built.
You have to clone people, teach them consistently, by some sort of automated teaching system maybe, to ensure a consistency of the results, preventing degradation of personnel quality - making a human machine, which will last for centuries.
And it has to be enforced for a few generations, to ensure that the system works, in a situation where they (people ancestors of the future crew) do not have to live that way - I have a few examples:
- feel free to continue
Dictatorship is the last problem you have to care about on generation ships with limited resources, where survival of the ship and success of the journey depends on all crew members working on that expedition job.
But which problem is that ship intended to solve, if it is survival after supernovae blast dictatorship is probably also not in first places of your problem list to care about and you allow freedoms where you can have them.
If the goal is just to have humans in other systems, without much care about which cultural values they will have, and if you are against just making artificial panspermia, send an artificial womb and a cloning facility - and you are done. (The example is a bit weak, and I could strengthen that situation to be more viable, but it is not the point here.)
So, which problem does a generation ship have to solve?
If it is the relocation of a high amount of peoples - you probably will have a possibility to keep already working systems.
If exporting values, which made that journey possible, is also a goal - you have to have enough people.
So the answer to your question has to be: have enough people.
From your previous question, where you considered the journey of 100 million of peoples - this is big enough to keep any currently known social system.
The exact amount of people needed for the journey - is determined can they develop or not, if they do then it is enough, if they are not able to do so, it is not enough. My personal preference is 20 million and above.
Space habitats could be a good start for a generation ship, as they, in fact, are such ships, which are happy where they are.
A generation ship has to have all social elements you care about, all environmental things:
- everything you enjoy or plan to have in your future terraformed planet if it is the plan.
Because if they do not have all these things the perception of what is normal will change over generations, to accommodate the current ship's environment, and you have to figure out an excuse - a reason, which will force them to do what they do not like. "Bhuye those stinky animals - they piss, they shit, no no no, f@!? them! Gimme delicious nutrient paste and cockroaches and that vodka!"
Have enough people, take more than you need, choose the system you like, live that system for some time, make referendum Brexit, leave those who do not like it, separate habitat, test for a few years if someone will change its mind completely and fly away after that.
Preparation. Planing. Testing.