What is the fate of the many nations that the message did not reach in the early days of Islam and in later times? Will they be held accountable for their transgression of innate matters, or are the remnants of previous messages sufficient to hold them accountable for them?

The intention is that the majority of humanity received the call and had the proof established against them through prophets and messengers or their followers. The existence of those who did not receive the call (Ahl al-Fatra - people of the interim period) is an assumption that does not detract from the wisdom of creation, nor from people's need for messengers. Allah will test Ahl al-Fatra in the Hereafter, because the predominant case is what matters, and because their existence completes the types and categories of creation and demonstrates Allah's justice and mercy.