The one problem which could be an issue is not being able to open an individual team's questionnaire until the Vision Assessment has been completed. My son had to complete the tasks in order (Profile, General Questionnaire, Medical Authorization, Medical Questionnaire, Vision Assessment Form, etc.) BEFORE being able to access other individual team questionnaires. But perhaps your son's situation could be different depending on the timing and delivery of the various questionnaires.
My son did not get specific addition medical documentation uploaded by the deadline (because I was too lazy to look for it) which seems to be OK, as long as the Medical Questionnaire itself has been completed. I figure if a team really needs physical therapy documents from when my son had Little League elbow they will request it again if it gets serious. And by serious I mean the 2020 MLB draft, not Little League elbow!