I don't even know what point you are trying to make now. Your example, Witcher 3, does exactly what you say should be a problem and is widely acclaimed. There is no problem with providing a strong conflict to sell the story and the game, while allowing the character to do side quests.
Regardless, even if it were a problem, solving it by removing the strong conflict is the exact backwards way of handling it. The best solution of all is to make the side quests relevant to the main quest. Why is having meaningless side quests the part of the equation you feel needs to be a constant?