As with everything, scope for discussion and questioning is *within reason*. Standard processes and procedures exist to streamline standard, everyday tasks so that needless discussion doesn't occur, and to minimize errors across collaborating units. Otherwise, the minutiae consume an absurd amount of resources, or whatever benefit might arise from the proposed improvement will be negated by the time spent in discussion.
Good companies will have education sessions to introduce employees to processes, and have onboarding materials. Usually, once you reach a meaningful level of experience, you're invited into discussions for modifying or improving processes. Those would be the appropriate forums for questioning approaches.
If you find yourself frequently being rebuffed when you bring up these ideas, it might be a good idea to create a standing, time-limited meeting for general clarifications with your manager (say, 30 minutes once a month). Then you have an appropriate outlet and are given voice, and your manager has a reasonable expectation that discussion will not spill over unduly.
