Hi Apeiron
Greetings to you too.
I don’t think you’ve done anything wrong by asking a question, or feeling puzzled. I appreciate your concern for the long-faring of pure Dhamma (and Vinaya).
To me your question is based on the philosophy of centralised control, or everyone agreeing and practising exactly the same way, which I do not see the Buddha tried to enforce. His advice for (a?) sangha (parisā?) to do away with minor rules if it deems fit, speaks to that, imo. The idea of centralised control has been promoted at least since the Third Buddhist Council. Its outcome was that, even if it may not specifically be stated as a goal, but I think it was made quite clear that was a goal.
The Buddha refused to appoint a successor, indicates to me that he didn’t even think of himself as the leader, but, as he said Dhamma and Vinaya would be the teacher when he had passed, as it always had. To me one person in charge speaks to centralised control, not faith in Dhamma and people’s wise reflection.
For me there is a core, which those with Right View would agree on and practice and there is periphery, with secondary things. In the words of Vinaya: Sīla (morality/ethics) - core and Ācāra (good habits) - superficial, secondary. I believe those people with Right View would agree on what was the core, which would be timeless (akāliko) and would know that all outside that core would be secondary and dependent on conditions.
Those who have not attained the Fruit of Stream Entry, (eradicated the First Three Fetters) may not see such a distinction and, if they did have the distinction, would certainly not agree on what was core and what not. Thus (attachment to) Rites and Rituals is maintained.
Those with wise reflection could be called ‘wise’ and Dhamma is to be discovered, each for themselves. Even so, I believe they would agree on what is the core and what is periphery. (This is opposite to the story of the First Council.)
I think everyone does follow their own belief, but those with Right View share the same essential beliefs. They have made the theory of Dhamma their own personal experience.
There is a place where the Buddha says to Ānanda, that disagreement over the Patimokkha (Vinaya) would be a trifling thing, but disagreement over what is the Path (or Way - the Fourth Noble Truth) would be for the detriment to the many for a long time. Thus the advice from the Buddha on comparing teachings (of the path) to ensure the longevity of the Dhamma and this does not seem to be done in the Buddhist Councils.
It is the sekkhiya sections of the Patimokkha that seem to have the most variation in number throughout the various Buddhist traditions. Regarding the monks’ rules, there is a place that mentions (about?) 150 rules. Without the sekkhiya, there are around 150. Sekkhiya are certainly minor rules, imo. For me, 4 Parajika and 13 Sanghadisesa (=17) are serious and cover sīla (morality/ethics) and the rest are minor and cover ācāra (good habits).
I hope that answers your question and eases your puzzlement.
Best wishes